http://subtiwiki.uni-goettingen.de/wiki//api.php?action=feedcontributions&feedformat=atom&user=Antelmann
SubtiWiki - User contributions [en]
2026-04-06T04:58:01Z
User contributions
MediaWiki 1.30.0
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=OhrR&diff=175843
OhrR
2012-09-06T08:51:09Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' transcription repressor of the ''[[ohrA]]'' gene <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''ohrR ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykmA''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || transcription repressor ([[MarR family]]) <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of ''[[ohrA]]'' expression <br/>in response to organic peroxides<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU13150 ohrR]<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 16 kDa, 6.364 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 441 bp, 147 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ohrA]]'', ''[[ohrB]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13172&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:ykmA_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ohrR_1381434_1381877_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ohrR_expression.png|500px]]<br />
|-<br />
|}<br />
<br />
__TOC__<br />
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<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[transcription factors and their control]]}},<br />
{{SubtiWiki category|[[resistance against oxidative and electrophile stress]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
<br />
=The [[OhrR regulon]]:=<br />
* ''[[ohrA]]''<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU13150<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ykmA.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13239]<br />
<br />
=== Additional information===<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' <br />
<br />
* '''Protein family:''' [[MarR family]]<br />
<br />
* '''Paralogous protein(s):'''<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:''' <br />
** senses organic peroxides and NaOCl, released from DNA upon oxidation of an active site cysteine<br />
** S-bacillithiolated by NaOCl and CHP stress on Cys-15, this results in release from the'' [[ohrA]]'' promoter {{PubMed|21749987}} <br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
** forms dimers<br />
<br />
* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot)<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1Z91 1Z91] (reduced form), [http://www.rcsb.org/pdb/explore.do?structureId=1Z9C 1Z9C] (complex with ''[[ohrA]]'' promoter) <br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/O34777 O34777]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU13150]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''ohrR'' {{PubMed|9696771}}<br />
<br />
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ohrR_1381434_1381877_-1 ohrR] {{PubMed|22383849}}<br />
<br />
* '''Sigma factor:''' [[SigA]] <br />
<br />
* '''Regulation:''' <br />
<br />
* '''Regulatory mechanism:''' <br />
<br />
* '''Additional information:'''<br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
[[John Helmann]], Cornell University, USA [http://www.micro.cornell.edu/research/labs/helmann-lab/index.cfm Homepage]<br />
<br />
[[Richard Brennan]], Houston, Texas, USA [http://www.mdanderson.org/departments/biochem/display.cfm?id=556ef368-6c81-4043-b74f350d41dd06cb&method=displayfull&pn=a8427ebd-d0ff-11d4-80fd00508b603a14 Homepage]<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
==Reviews==<br />
<pubmed>22797754 </pubmed><br />
Antelmann H, Helmann JD.<br />
Thiol-based redox switches and gene regulation.<br />
Antioxid Redox Signal. 2011,14:1049-63.<br />
{{PubMed|20626317}}<br />
<pubmed>19575568 20094649 </pubmed><br />
<br />
==Original Publications==<br />
<pubmed>21749987,16209951,18487332,17660290,17502599,12486061,11418552,18586944,11983871,18363800,19129220 9696771 21749987 22797754 </pubmed><br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=BrxA&diff=175840
BrxA
2012-09-06T08:47:54Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' disulfide isomerase, putative bacilliredoxin <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''yphP''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || disulfide isomerase, putative bacilliredoxin<br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU21860 yphP]<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 15 kDa, 4.619 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 432 bp, 144 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ypiP]]'', ''[[ilvD]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14104&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:yphP_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yphP_2300221_2300655_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yphP_expression.png|500px]]<br />
|-<br />
|}<br />
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__TOC__<br />
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= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[poorly characterized/ putative enzymes]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU21860<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yphP.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11614]<br />
<br />
=== Additional information===<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' <br />
<br />
* '''Protein family:''' scpA family (according to Swiss-Prot)<br />
<br />
* '''Paralogous protein(s):''' [[yqiW]]<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' contains an CxC redox motif [http://www.ncbi.nlm.nih.gov/pubmed/20308541]<br />
<br />
* '''Modification:''' <br />
** S-bacillithiolation upon hypochlorite stress on Cys-53 {{PubMed|21749987}} <br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
<br />
* '''Localization:'''<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3FHK 3FHK] {{PubMed|19653655}}<br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P54170 P54170]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU21860]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''yphP'' (according to [http://dbtbs.hgc.jp/COG/prom/yphP.html DBTBS])<br />
<br />
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yphP_2300221_2300655_-1 yphP] {{PubMed|22383849}}<br />
<br />
* '''Sigma factor:''' <br />
<br />
* '''Regulation:''' <br />
<br />
* '''Regulatory mechanism:''' <br />
<br />
* '''Additional information:'''<br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
=Your additional remarks=<br />
[[YpdA]], [[YqiW]], [[YphP]] and [[YtxJ]] co-occur in those species predicted to synthesize bacillithiol.<br />
<br />
=References=<br />
<pubmed> 22938038,19653655 20308541 21749987</pubmed><br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=SerA&diff=175838
SerA
2012-09-06T08:45:56Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' phosphoglycerate dehydrogenase <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''serA''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphoglycerate dehydrogenase<br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of serine<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU23070 serA]<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/ala_gly_ser.html Ala, Gly, Ser]'''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56 kDa, 5.617 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1575 bp, 525 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ypzE]]'', ''[[aroC]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14239&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:serA_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=serA_2411086_2412663_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:serA_expression.png|500px]]<br />
|-<br />
|}<br />
<br />
__TOC__<br />
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<br/><br/><br/><br/><br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[biosynthesis/ acquisition of amino acids]]}},<br />
{{SubtiWiki category|[[membrane proteins]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU23070<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/serA.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10509]<br />
<br />
=== Additional information===<br />
<br />
<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' 3-phospho-D-glycerate + NAD<sup>+</sup> = 3-phosphonooxypyruvate + NADH (according to Swiss-Prot) <br />
<br />
* '''Protein family:''' D-isomer specific 2-hydroxyacid dehydrogenase family (according to Swiss-Prot)<br />
<br />
* '''Paralogous protein(s):'''<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:''' <br />
** S-cysteinylation after diamide stress (C410)[http://www.ncbi.nlm.nih.gov/sites/entrez/17611193 PubMed]<br />
** active site Cys410 is S-bacillithiolated by NaOCl stress in B. subtilis and other Bacillus species {{PubMed|21749987}} {{PubMed|22938038}}<br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
<br />
* '''[[Localization]]:''' membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1YBA 1YBA] (from ''E. coli'', 30% identity, 52% similarity) {{PubMed|15823035}}<br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P35136 P35136]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU23070]<br />
<br />
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.95 1.1.1.95]<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''serA'' {{PubMed|7934830}}<br />
<br />
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=serA_2411086_2412663_1 serA] {{PubMed|22383849}}<br />
<br />
* '''Sigma factor:''' <br />
<br />
* '''Regulation:''' <br />
<br />
* '''Regulatory mechanism:''' <br />
<br />
* '''Additional information:'''<br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:''' pGP187 (in [[pAC7]]), available in [[Stülke]] lab<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
<pubmed>22938038,17611193,7934830 ,18763711,15823035 21749987 </pubmed><br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=SerA&diff=175837
SerA
2012-09-06T08:45:14Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' phosphoglycerate dehydrogenase <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''serA''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphoglycerate dehydrogenase<br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of serine<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU23070 serA]<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/ala_gly_ser.html Ala, Gly, Ser]'''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56 kDa, 5.617 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1575 bp, 525 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ypzE]]'', ''[[aroC]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14239&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:serA_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=serA_2411086_2412663_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:serA_expression.png|500px]]<br />
|-<br />
|}<br />
<br />
__TOC__<br />
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<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br />
<br />
<br/><br/><br/><br/><br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[biosynthesis/ acquisition of amino acids]]}},<br />
{{SubtiWiki category|[[membrane proteins]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU23070<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/serA.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10509]<br />
<br />
=== Additional information===<br />
<br />
<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' 3-phospho-D-glycerate + NAD<sup>+</sup> = 3-phosphonooxypyruvate + NADH (according to Swiss-Prot) <br />
<br />
* '''Protein family:''' D-isomer specific 2-hydroxyacid dehydrogenase family (according to Swiss-Prot)<br />
<br />
* '''Paralogous protein(s):'''<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:''' <br />
** S-cysteinylation after diamide stress (C410)[http://www.ncbi.nlm.nih.gov/sites/entrez/17611193 PubMed]<br />
** active site Cys410 is S-bacillithiolated by NaOCl stress in B. subtilis and other Bacillus species {{PubMed|21749987}} {{PubMed|22938038}}<br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
<br />
* '''[[Localization]]:''' membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1YBA 1YBA] (from ''E. coli'', 30% identity, 52% similarity) {{PubMed|15823035}}<br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P35136 P35136]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU23070]<br />
<br />
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.95 1.1.1.95]<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''serA'' {{PubMed|7934830}}<br />
<br />
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=serA_2411086_2412663_1 serA] {{PubMed|22383849}}<br />
<br />
* '''Sigma factor:''' <br />
<br />
* '''Regulation:''' <br />
<br />
* '''Regulatory mechanism:''' <br />
<br />
* '''Additional information:'''<br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:''' pGP187 (in [[pAC7]]), available in [[Stülke]] lab<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
<pubmed>17611193,7934830 ,18763711,15823035 21749987 </pubmed><br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=PpaC&diff=175835
PpaC
2012-09-06T08:42:59Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' inorganic pyrophosphatase <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''ppaC''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yybQ ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed] <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || inorganic pyrophosphatase<br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || recovery of phosphate ions from pyrophosphate <br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU40550 ppaC]<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 4.513 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 927 bp, 309 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[hypR]]'', ''[[yybP]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16092&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:ppaC_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ppaC_4168204_4169133_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ppaC_expression.png|500px]]<br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[phosphate metabolism]]}},<br />
{{SubtiWiki category|[[essential genes]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU40550<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ppaC.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10014]<br />
<br />
=== Additional information===<br />
<br />
<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' Diphosphate + H<sub>2</sub>O = 2 phosphate (according to Swiss-Prot) <br />
<br />
* '''Protein family:''' PPase class C family (according to Swiss-Prot)<br />
<br />
* '''Paralogous protein(s):'''<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:''' <br />
** S-cysteinylation after diamide stress (C158) [http://www.ncbi.nlm.nih.gov/sites/entrez/17611193 PubMed]<br />
** Cys158 is S-bacillithiolated by NaOCl stress in B. subtilis and other Bacillus species {{PubMed|21749987}} {{PubMed|21749987}}<br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
<br />
* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot)<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2HAW 2HAW] (complex with substrate analogue p-nitrophosphate), [http://www.rcsb.org/pdb/explore.do?structureId=1WPM 1WPM] <br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P37487 P37487]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40550]<br />
<br />
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.6.1.1 3.6.1.1]<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''ppaC'' (according to [http://dbtbs.hgc.jp/COG/prom/ppaC.html DBTBS])<br />
<br />
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ppaC_4168204_4169133_1 ppaC] {{PubMed|22383849}}<br />
<br />
* '''Sigma factor:''' <br />
<br />
* '''Regulation:''' <br />
<br />
* '''Regulatory mechanism:''' <br />
<br />
* '''Additional information:'''<br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
<pubmed>22938038,21749987,15533045,17611193,9845334 9782505 11342544, 9633597 21749987</pubmed><br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=PpaC&diff=175834
PpaC
2012-09-06T08:40:39Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' inorganic pyrophosphatase <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''ppaC''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yybQ ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed] <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || inorganic pyrophosphatase<br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || recovery of phosphate ions from pyrophosphate <br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU40550 ppaC]<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 4.513 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 927 bp, 309 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[hypR]]'', ''[[yybP]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16092&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:ppaC_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ppaC_4168204_4169133_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ppaC_expression.png|500px]]<br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[phosphate metabolism]]}},<br />
{{SubtiWiki category|[[essential genes]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU40550<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ppaC.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10014]<br />
<br />
=== Additional information===<br />
<br />
<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' Diphosphate + H<sub>2</sub>O = 2 phosphate (according to Swiss-Prot) <br />
<br />
* '''Protein family:''' PPase class C family (according to Swiss-Prot)<br />
<br />
* '''Paralogous protein(s):'''<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:''' <br />
** S-cysteinylation after diamide stress (C158) [http://www.ncbi.nlm.nih.gov/sites/entrez/17611193 PubMed]<br />
** Cys158 is S-bacillithiolated by NaOCl stress in B. subtilis and other Bacillus species {{PubMed|21749987}} {{PubMed|21749987}}<br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
<br />
* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot)<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2HAW 2HAW] (complex with substrate analogue p-nitrophosphate), [http://www.rcsb.org/pdb/explore.do?structureId=1WPM 1WPM] <br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P37487 P37487]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40550]<br />
<br />
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.6.1.1 3.6.1.1]<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''ppaC'' (according to [http://dbtbs.hgc.jp/COG/prom/ppaC.html DBTBS])<br />
<br />
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ppaC_4168204_4169133_1 ppaC] {{PubMed|22383849}}<br />
<br />
* '''Sigma factor:''' <br />
<br />
* '''Regulation:''' <br />
<br />
* '''Regulatory mechanism:''' <br />
<br />
* '''Additional information:'''<br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
<pubmed>21749987,15533045,17611193,9845334 9782505 11342544, 9633597 21749987</pubmed><br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=MetE&diff=175833
MetE
2012-09-06T08:37:21Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' methionine synthase <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''metE''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''metC ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || methionine synthase<br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of methionine<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU13180 metE]<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/cys_meth_and_sulfate_assimilation.html Cys, Met & Sulfate assimilation]'''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 86 kDa, 4.839 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2286 bp, 762 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[guaD]]'', ''[[ispA]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13175&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:metE_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=metE_1383320_1385608_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:metE_expression.png|500px]]<br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br />
<br />
<br/><br/><br/><br/><br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[biosynthesis/ acquisition of amino acids]]}},<br />
{{SubtiWiki category|[[phosphoproteins]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[S-box]]}}<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU13180<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' no entry<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12616]<br />
<br />
=== Additional information===<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' 5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine = tetrahydropteroyltri-L-glutamate + L-methionine (according to Swiss-Prot) <br />
<br />
* '''Protein family:''' vitamin-B12 independent methionine synthase family (according to Swiss-Prot)<br />
<br />
* '''Paralogous protein(s):'''<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:''' <br />
**phosphorylated on ser/ thr/ tyr [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed], S-cysteinylation after diamide stress (C719) [http://www.ncbi.nlm.nih.gov/sites/entrez/17611193 PubMed]<br />
** Cys719 and Cys730 are S-bacillithiolated by NaOCl stress in B. subtilis and other Bacillus species {{PubMed|21749987}} {{PubMed|22938038}}<br />
** MetE is generally most strongly S-bacillithiolated by NaOCl stress in B. subtilis and other Bacillus species {{PubMed|21749987}} {{PubMed|22938038}}<br />
<br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
<br />
* '''[[Localization]]:'''<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1T7L 1T7L] (from ''Thermotoga maritima'', 44% identity, 61% similarity) {{PubMed|15630480}}<br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P80877 P80877]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU13180]<br />
<br />
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.1.1.14 2.1.1.14]<br />
<br />
=== Additional information===<br />
<br />
:* subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''metE''<br />
<br />
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=metE_1383320_1385608_-1 metE] {{PubMed|22383849}}<br />
<br />
* '''Sigma factor:''' <br />
<br />
* '''Regulation:''' <br />
** repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed] <br />
** repressed by methionine (about 1000-fold)([[S-box]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10094622 PubMed]<br />
<br />
* '''Regulatory mechanism:''' [[S-box]]: transcription termination/ antitermination, the [[S-box]] [[riboswitch]] binds S-adenosylmethionine resulting in termination [http://www.ncbi.nlm.nih.gov/sites/entrez/10094622 PubMed]<br />
<br />
* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]<br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
'''Additional publications:''' {{PubMed|21749987}}<br />
<pubmed>22938038,21749987,19258532,16194229,10094622,17611193,18039762 ,17726680 12107147</pubmed><br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=MetE&diff=175832
MetE
2012-09-06T08:35:08Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' methionine synthase <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''metE''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''metC ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || methionine synthase<br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of methionine<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU13180 metE]<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/cys_meth_and_sulfate_assimilation.html Cys, Met & Sulfate assimilation]'''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 86 kDa, 4.839 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2286 bp, 762 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[guaD]]'', ''[[ispA]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13175&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:metE_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=metE_1383320_1385608_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:metE_expression.png|500px]]<br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br />
<br />
<br/><br/><br/><br/><br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[biosynthesis/ acquisition of amino acids]]}},<br />
{{SubtiWiki category|[[phosphoproteins]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[S-box]]}}<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU13180<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' no entry<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12616]<br />
<br />
=== Additional information===<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' 5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine = tetrahydropteroyltri-L-glutamate + L-methionine (according to Swiss-Prot) <br />
<br />
* '''Protein family:''' vitamin-B12 independent methionine synthase family (according to Swiss-Prot)<br />
<br />
* '''Paralogous protein(s):'''<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:''' <br />
**phosphorylated on ser/ thr/ tyr [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed], S-cysteinylation after diamide stress (C719) [http://www.ncbi.nlm.nih.gov/sites/entrez/17611193 PubMed]<br />
** Cys719 and Cys730 are S-bacillithiolated by NaOCl stress in B. subtilis and other Bacillus species {{PubMed|21749987}} {{PubMed|22938038}}<br />
** MetE is generally most strongly S-bacillithiolated by NaOCl stress in B. subtilis and other Bacillus species {{PubMed|21749987}} {{PubMed|22938038}}<br />
<br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
<br />
* '''[[Localization]]:'''<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1T7L 1T7L] (from ''Thermotoga maritima'', 44% identity, 61% similarity) {{PubMed|15630480}}<br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P80877 P80877]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU13180]<br />
<br />
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.1.1.14 2.1.1.14]<br />
<br />
=== Additional information===<br />
<br />
:* subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''metE''<br />
<br />
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=metE_1383320_1385608_-1 metE] {{PubMed|22383849}}<br />
<br />
* '''Sigma factor:''' <br />
<br />
* '''Regulation:''' <br />
** repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed] <br />
** repressed by methionine (about 1000-fold)([[S-box]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10094622 PubMed]<br />
<br />
* '''Regulatory mechanism:''' [[S-box]]: transcription termination/ antitermination, the [[S-box]] [[riboswitch]] binds S-adenosylmethionine resulting in termination [http://www.ncbi.nlm.nih.gov/sites/entrez/10094622 PubMed]<br />
<br />
* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]<br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
'''Additional publications:''' {{PubMed|21749987}}<br />
<pubmed>22938038,19258532,16194229,10094622,17611193,18039762 ,17726680 12107147</pubmed><br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=ThrS&diff=175831
ThrS
2012-09-06T08:31:04Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' threonyl-tRNA synthetase (major) <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''thrS''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || threonyl-tRNA synthetase (major)<br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || translation <br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU28950 thrS]<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/tRNA_charging.html tRNA charging]'''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 73 kDa, 5.214 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1929 bp, 643 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ysaA]]'', ''[[ytxC]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14855&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|-<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:thrS_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=thrS_2959257_2961188_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:thrS_expression.png|500px]]<br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br />
<br/><br/><br/><br/><br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[translation]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[T-box]]}}<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU28950<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/thrS.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10362]<br />
<br />
=== Additional information===<br />
<br />
<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + L-threonyl-tRNA(Thr) (according to Swiss-Prot) <br />
<br />
* '''Protein family:''' class-II aminoacyl-tRNA synthetase family (according to Swiss-Prot)<br />
<br />
* '''Paralogous protein(s):''' [[ThrZ]], one of the two proteins has to be present for viability [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 PubMed]<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:'''Cys573 is S-bacillithiolated by NaOCl stress [http://www.ncbi.nlm.nih.gov/sites/entrez/22938038 PubMed]<br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
<br />
* '''[[Localization]]:'''<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1TJE 1TJE] (from ''Escherichia coli'', 44% identity, 63% similarity) {{PubMed|15525511}}<br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P18255 P18255]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU28950]<br />
<br />
* '''E.C. number:''' [http://www.expasy.org/enzyme/6.1.1.3 6.1.1.3]<br />
<br />
=== Additional information===<br />
<br />
:* subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''[[thrS]]'' {{PubMed|8969504}} <br />
<br />
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=thrS_2959257_2961188_-1 thrS] {{PubMed|22383849}}<br />
<br />
* '''Sigma factor:''' [[SigA]] {{PubMed|8288542}} <br />
<br />
* '''Regulation:''' <br />
** induced by threonine limitation ([[T-box]]) {{PubMed|19258532,8288542}} <br />
** expression transiently increases in the forespore {{PubMed|22848659}}<br />
<br />
* '''Regulatory mechanism:''' <br />
** [[T-box]]: [[RNA switch]], transcriptional antitermination {{PubMed|19258532}} <br />
<br />
* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]<br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
<pubmed>22938038,8288542,1379177,19258532,7476165,12136084,8969504 ,17114254, 22848659</pubmed><br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=QueF&diff=175830
QueF
2012-09-06T08:28:05Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' nitrile reductase (NADPH-dependent 7-cyano-7-deazaguanine reductase), synthesis of the modified ribonucleotide queuosine <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''queF ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykvM''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || nitrile reductase<br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || tRNA modification<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU13750 queF]<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 19 kDa, 4.927 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 495 bp, 165 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[queE]]'', ''[[ykvN]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13248&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:ykvM_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=queF_1441291_1441788_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:queF_expression.png|500px]]<br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[translation]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[preQ1 riboswitch]]}}<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU13750<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' no entry<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13315]<br />
<br />
=== Additional information===<br />
<br />
<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' 7-aminomethyl-7-carbaguanine + 2 NADP<sup>+</sup> = 7-cyano-7-carbaguanine + 2 NADPH (according to Swiss-Prot) <br />
<br />
* '''Protein family:''' QueF type 1 subfamily (according to Swiss-Prot)<br />
<br />
* '''Paralogous protein(s):'''<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:''' active site Cys56 is S-bacillithiolated by NaOCl stress {{PubMed|22938038}} <br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
<br />
* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot)<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?structureId=4F8b 4F8B] (covalent thioimide intermediate of the unimodular nitrile reductase [[QueF]]) {{PubMed|22787148}}<br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/O31678 O31678]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU13750]<br />
<br />
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.7.1.13 1.7.1.13]<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''[[queC]]-[[queD]]-[[queE]]-[[queF]]'' {{PubMed|14660578}}<br />
<br />
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=queF_1441291_1441788_1 queF] {{PubMed|22383849}}<br />
<br />
* '''Sigma factor:''' <br />
<br />
* '''Regulation:''' <br />
** repressed in the presence of queuosine ([[preQ1 riboswitch]]) {{PubMed|19285444}} <br />
<br />
* '''Regulatory mechanism:''' <br />
** [[preQ1 riboswitch]]: transcriptional antitermination in the absence of queuosine {{PubMed|19285444}} <br />
<br />
* '''Additional information:'''<br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
<pubmed>22938038,14660578,15767583 16511203 ,17929836 19285444 17384645 22787148 </pubmed><br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=YumC&diff=175829
YumC
2012-09-06T08:24:12Z
<p>Antelmann: /* Extended information on the protein */</p>
<hr />
<div>* '''Description:''' ferredoxin-NAD(P)+ oxidoreductase<br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''yumC''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed] <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || ferredoxin-NAD(P)+ oxidoreductase<br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || redox reactions that involve ferredoxin<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU32110 yumC]<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 36 kDa, 5.573 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 996 bp, 332 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yumB]]'', ''[[yuzG]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15201&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:yumC_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yumC_3301586_3302584_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yumC_expression.png|500px]]<br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[electron transport/ other]]}},<br />
{{SubtiWiki category|[[essential genes]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU32110<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' no entry<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12391]<br />
<br />
=== Additional information===<br />
<br />
<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' 2 reduced ferredoxin + NADP<sup>+</sup> + H<sup>+</sup> = 2 oxidized ferredoxin + NADPH (according to Swiss-Prot) <br />
<br />
* '''Protein family:''' ferredoxin--NADP reductase type 2 family (according to Swiss-Prot)http://www.ncbi.nlm.nih.gov/pubmed<br />
<br />
* '''Paralogous protein(s):''' [[YcgT]]<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:''' active site Cys85 is S-bacillithiolated by NaOCl stress in B. subtilis and other Bacillus species[http://www.ncbi.nlm.nih.gov/pubmed/22938038 PubMed]<br />
<br />
* '''Cofactor(s):''' FAD, NADPH {{PubMed|20878669}}<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''Interactions:''' dimeric protein {{PubMed|20878669}}<br />
<br />
* '''Localization:'''<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' [http://www.pdb.org/pdb/search/structidSearch.do?structureId=3LZW 3LZW] {{PubMed|20878669}}<br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/O05268 O05268]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU32110]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' <br />
<br />
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yumC_3301586_3302584_1 yumC] {{PubMed|22383849}}<br />
<br />
* '''Sigma factor:''' <br />
<br />
* '''Regulation:''' <br />
<br />
* '''Regulatory mechanism:''' <br />
<br />
* '''Additional information:'''<br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
<pubmed>22938038, 20208166, 20878669, 19162251, 15252706 </pubmed><br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=YumC&diff=175828
YumC
2012-09-06T08:23:30Z
<p>Antelmann: /* Extended information on the protein */</p>
<hr />
<div>* '''Description:''' ferredoxin-NAD(P)+ oxidoreductase<br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''yumC''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed] <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || ferredoxin-NAD(P)+ oxidoreductase<br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || redox reactions that involve ferredoxin<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU32110 yumC]<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 36 kDa, 5.573 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 996 bp, 332 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yumB]]'', ''[[yuzG]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15201&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:yumC_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yumC_3301586_3302584_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yumC_expression.png|500px]]<br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[electron transport/ other]]}},<br />
{{SubtiWiki category|[[essential genes]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU32110<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' no entry<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12391]<br />
<br />
=== Additional information===<br />
<br />
<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' 2 reduced ferredoxin + NADP<sup>+</sup> + H<sup>+</sup> = 2 oxidized ferredoxin + NADPH (according to Swiss-Prot) <br />
<br />
* '''Protein family:''' ferredoxin--NADP reductase type 2 family (according to Swiss-Prot)http://www.ncbi.nlm.nih.gov/pubmed<br />
<br />
* '''Paralogous protein(s):''' [[YcgT]]<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:''' active site Cys85 is S-bacillithiolated by NaOCl stress in B. subtilis and other Bacillus species[http://www.ncbi.nlm.nih.gov/pubmed/22938038 PubMed]<br />
<br />
* '''Cofactor(s):''' FAD, NADPH {{PubMed|20878669}}<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''Interactions:''' dimeric protein {{PubMed|20878669}}<br />
<br />
* '''Localization:'''<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' [http://www.pdb.org/pdb/search/structidSearch.do?structureId=3LZW 3LZW] {{PubMed|20878669}}<br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/O05268 O05268]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU32110]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' <br />
<br />
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yumC_3301586_3302584_1 yumC] {{PubMed|22383849}}<br />
<br />
* '''Sigma factor:''' <br />
<br />
* '''Regulation:''' <br />
<br />
* '''Regulatory mechanism:''' <br />
<br />
* '''Additional information:'''<br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
<pubmed>22938038, 20208166, 20878669, 19162251, 15252706 </pubmed><br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=YumC&diff=175827
YumC
2012-09-06T08:22:37Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' ferredoxin-NAD(P)+ oxidoreductase<br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''yumC''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed] <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || ferredoxin-NAD(P)+ oxidoreductase<br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || redox reactions that involve ferredoxin<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU32110 yumC]<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 36 kDa, 5.573 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 996 bp, 332 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yumB]]'', ''[[yuzG]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15201&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:yumC_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yumC_3301586_3302584_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yumC_expression.png|500px]]<br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[electron transport/ other]]}},<br />
{{SubtiWiki category|[[essential genes]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU32110<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' no entry<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12391]<br />
<br />
=== Additional information===<br />
<br />
<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' 2 reduced ferredoxin + NADP<sup>+</sup> + H<sup>+</sup> = 2 oxidized ferredoxin + NADPH (according to Swiss-Prot) <br />
<br />
* '''Protein family:''' ferredoxin--NADP reductase type 2 family (according to Swiss-Prot)http://www.ncbi.nlm.nih.gov/pubmed<br />
<br />
* '''Paralogous protein(s):''' [[YcgT]]<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:'''<br />
*** active site Cys85 is S-bacillithiolated by NaOCl stress in B. subtilis and other Bacillus species[http://www.ncbi.nlm.nih.gov/pubmed/22938038 PubMed]<br />
<br />
* '''Cofactor(s):''' FAD, NADPH {{PubMed|20878669}}<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''Interactions:''' dimeric protein {{PubMed|20878669}}<br />
<br />
* '''Localization:'''<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' [http://www.pdb.org/pdb/search/structidSearch.do?structureId=3LZW 3LZW] {{PubMed|20878669}}<br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/O05268 O05268]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU32110]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' <br />
<br />
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yumC_3301586_3302584_1 yumC] {{PubMed|22383849}}<br />
<br />
* '''Sigma factor:''' <br />
<br />
* '''Regulation:''' <br />
<br />
* '''Regulatory mechanism:''' <br />
<br />
* '''Additional information:'''<br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
<pubmed>22938038, 20208166, 20878669, 19162251, 15252706 </pubmed><br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=TufA&diff=175826
TufA
2012-09-06T08:18:09Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' elongation factor Tu <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''tufA''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed] <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || elongation factor Tu<br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || [[translation]] <br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU01130 tufA]<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/TufA TufA]<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 43 kDa, 4.723 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1188 bp, 396 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[fusA]]'', ''[[ybaC]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11889&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:tufA_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=tufA_132882_134072_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:tufA_expression.png|500px]]<br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[translation]]}},<br />
{{SubtiWiki category|[[essential genes]]}},<br />
{{SubtiWiki category|[[membrane proteins]]}},<br />
{{SubtiWiki category|[[phosphoproteins]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[stringent response]]}}<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU01130<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' no entry<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11056]<br />
<br />
=== Additional information===<br />
<br />
<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' <br />
<br />
* '''Protein family:''' EF-Tu/EF-1A subfamily (according to Swiss-Prot)<br />
<br />
* '''Paralogous protein(s):'''<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:''' phosphorylated on Thr-384 by [[PrkC]], dephosphorylated by [[PrpC]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19246764 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]<br />
** Cys83 is S-bacillithiolated in B. subtilis and other Bacillus species [http://www.ncbi.nlm.nih.gov/pubmed/22938038 PubMed]<br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
** [[MreB]]-[[TufA]] {{PubMed|20133608}} <br />
<br />
* '''[[Localization]]:''' <br />
** EF-Tu localizes in a helical pattern underneath the cell membrane and colocalizes with [[MreB]] {{PubMed|20133608}}<br />
** membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' <br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P33166 P33166]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01130]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' <br />
<br />
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=tufA_132882_134072_1 tufA] {{PubMed|22383849}}<br />
<br />
* '''Sigma factor:''' <br />
<br />
* '''Regulation:''' <br />
** [[RelA]] dependent downregulation (Class I) during stringent response {{PubMed|11948165}}<br />
<br />
* '''Regulatory mechanism:''' <br />
<br />
* '''Additional information:'''<br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:''' <br />
** for expression/ purification from ''B. subtilis'' with N-terminal Strep-tag, for [[SPINE]], in [[pGP380]]: pGP839, available in [[Stülke]] lab<br />
** for expression/ purification from ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP847, available in [[Stülke]] lab<br />
<br />
<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
<pubmed>22938038,19246764,20133608 , 19246764, 17726680, 18763711 </pubmed><br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=AroA&diff=175825
AroA
2012-09-06T08:15:31Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase / chorismate mutase-isozyme 3 <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''aroA''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''aroG ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase /<br />
chorismate mutase-isozyme 3<br />
<br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of aromatic amino acids<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU29750 aroA]<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/phenyl_tyr_tryp.html Phe, Tyr, Trp]'''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 39 kDa, 5.341 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1074 bp, 358 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ccpA]]'', ''[[ytxJ]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14953&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:aroA_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=aroA_3045445_3046521_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:aroA_expression.png|500px]]<br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br />
<br />
<br/><br/><br/><br/><br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[biosynthesis/ acquisition of amino acids]]}},<br />
{{SubtiWiki category|[[phosphoproteins]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU29750<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/aroA.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10375]<br />
<br />
=== Additional information===<br />
<br />
<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' Phosphoenolpyruvate + D-erythrose 4-phosphate + H<sub>2</sub>O = 3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate + phosphate (according to Swiss-Prot) <br />
<br />
* '''Protein family:''' class-I DAHP synthetase family (according to Swiss-Prot)<br />
<br />
* '''Paralogous protein(s):'''<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:''' <br />
** phosphorylation on Ser-2 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]<br />
** phosphorylation on Thr-4 [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]<br />
** phosphorylated on Arg-45 and Arg-301 {{PubMed|22517742}}<br />
** Cys126 is S-bacillithiolated by NaOCl stress in B. subtilis and other Bacillus species [http://www.ncbi.nlm.nih.gov/sites/entrez/22938038 PubMed]<br />
<br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:''' subject to feedback inhibition [http://www.ncbi.nlm.nih.gov/sites/entrez/19258532 PubMed]<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
<br />
* '''[[Localization]]:'''<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1VR6 1VR6] (from ''Thermotoga maritima'', 51% identity, 68% similarity)<br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P39912 P39912]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29750]<br />
<br />
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.5.1.54 2.5.1.54] 5 and 5.4.99.5<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''[[aroA]]'' {{PubMed|9387221}} <br />
<br />
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=aroA_3045445_3046521_-1 aroA] {{PubMed|22383849}}<br />
<br />
* '''Sigma factor:''' <br />
<br />
* '''Regulation:''' <br />
<br />
* '''Regulatory mechanism:''' <br />
<br />
* '''Additional information:''' subject to feedback inhibition [http://www.ncbi.nlm.nih.gov/sites/entrez/19258532 PubMed]<br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
<pubmed>22938038,9387221,19258532 ,17726680 17218307, 22517742</pubmed><br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=GuaB&diff=175824
GuaB
2012-09-06T08:11:38Z
<p>Antelmann: /* References */</p>
<hr />
<div>* '''Description:''' IMP dehydrogenase <br/><br/><br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''guaB''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''guaA ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed] <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || IMP dehydrogenase<br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of GMP<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU00090 GuaB]<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/purine_biosynthesis.html Purine synthesis], [http://subtiwiki.uni-goettingen.de/pathways/gene_regulation_nucleotides.html Nucleotides (regulation)]'''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 6.168 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1464 bp, 488 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaC]]'', ''[[dacA]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11785&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:guaB_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=guaB_15915_17381_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:guaB_expression.png|500px]]<br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br />
<br />
<br/><br/><br/><br/><br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[biosynthesis/ acquisition of nucleotides]]}},<br />
{{SubtiWiki category|[[essential genes]]}},<br />
{{SubtiWiki category|[[phosphoproteins]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[CodY regulon]]}}<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU00090<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/guaB.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10073]<br />
<br />
=== Additional information===<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' Inosine 5'-phosphate + NAD<sup>+</sup> + H<sub>2</sub>O = xanthosine 5'-phosphate + NADH (according to Swiss-Prot) <br />
<br />
* '''Protein family:''' IMPDH/GMPR family (according to Swiss-Prot)<br />
<br />
* '''Paralogous protein(s):'''<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:''' <br />
** phosphorylated (STY) [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]<br />
** Cys308 is S-cysteinylated after diamide stress [http://www.ncbi.nlm.nih.gov/pubmed/17611193 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]<br />
** Cys308 is S-bacillithiolated by NaOCl stress in B. subtilis and other Bacillus species [http://www.ncbi.nlm.nih.gov/pubmed/22938038 PubMed] <br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
** inhibition of enzymatic activity by (p)ppGpp during the ´stringent response´{{PubMed|6111556}}<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
<br />
* '''[[Localization]]:'''<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1VRD 1VRD] (from ''Thermotoga maritima msb8'', 60% identity, 80% similarity)<br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P21879 P21879]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00090]<br />
<br />
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.205 1.1.1.205]<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''guaB'' {{PubMed|22383849}} <br />
<br />
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=guaB_15915_17381_1 guaB] {{PubMed|22383849}}<br />
<br />
* '''Sigma factor:''' <br />
<br />
* '''Regulation:''' <br />
** activated during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]<br />
<br />
* '''Regulatory mechanism:''' <br />
** [[CodY]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]<br />
<br />
* '''Additional information:''' <br />
** the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]<br />
** inhibition of enzymatic activity by (p)ppGpp during the ´stringent response´{{PubMed|6111556}}<br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
** purification from ''B. subtilis'' with an N-terminal Strep-tag, for [[SPINE]], (in [[pGP380]]): pGP901, available in [[Stülke]] lab<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
<pubmed>22938038,17611193,12884008,1722815,,12618455,17726680 17726680 6111556 </pubmed><br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/PMID PubMed]<br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=GuaB&diff=175823
GuaB
2012-09-06T08:10:47Z
<p>Antelmann: /* Extended information on the protein */</p>
<hr />
<div>* '''Description:''' IMP dehydrogenase <br/><br/><br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''guaB''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''guaA ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed] <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || IMP dehydrogenase<br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of GMP<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU00090 GuaB]<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/purine_biosynthesis.html Purine synthesis], [http://subtiwiki.uni-goettingen.de/pathways/gene_regulation_nucleotides.html Nucleotides (regulation)]'''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 6.168 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1464 bp, 488 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaC]]'', ''[[dacA]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11785&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:guaB_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=guaB_15915_17381_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:guaB_expression.png|500px]]<br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br />
<br />
<br/><br/><br/><br/><br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[biosynthesis/ acquisition of nucleotides]]}},<br />
{{SubtiWiki category|[[essential genes]]}},<br />
{{SubtiWiki category|[[phosphoproteins]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[CodY regulon]]}}<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU00090<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/guaB.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10073]<br />
<br />
=== Additional information===<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' Inosine 5'-phosphate + NAD<sup>+</sup> + H<sub>2</sub>O = xanthosine 5'-phosphate + NADH (according to Swiss-Prot) <br />
<br />
* '''Protein family:''' IMPDH/GMPR family (according to Swiss-Prot)<br />
<br />
* '''Paralogous protein(s):'''<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:''' <br />
** phosphorylated (STY) [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]<br />
** Cys308 is S-cysteinylated after diamide stress [http://www.ncbi.nlm.nih.gov/pubmed/17611193 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]<br />
** Cys308 is S-bacillithiolated by NaOCl stress in B. subtilis and other Bacillus species [http://www.ncbi.nlm.nih.gov/pubmed/22938038 PubMed] <br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
** inhibition of enzymatic activity by (p)ppGpp during the ´stringent response´{{PubMed|6111556}}<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
<br />
* '''[[Localization]]:'''<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1VRD 1VRD] (from ''Thermotoga maritima msb8'', 60% identity, 80% similarity)<br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P21879 P21879]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00090]<br />
<br />
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.205 1.1.1.205]<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''guaB'' {{PubMed|22383849}} <br />
<br />
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=guaB_15915_17381_1 guaB] {{PubMed|22383849}}<br />
<br />
* '''Sigma factor:''' <br />
<br />
* '''Regulation:''' <br />
** activated during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]<br />
<br />
* '''Regulatory mechanism:''' <br />
** [[CodY]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]<br />
<br />
* '''Additional information:''' <br />
** the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]<br />
** inhibition of enzymatic activity by (p)ppGpp during the ´stringent response´{{PubMed|6111556}}<br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
** purification from ''B. subtilis'' with an N-terminal Strep-tag, for [[SPINE]], (in [[pGP380]]): pGP901, available in [[Stülke]] lab<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
<pubmed>17611193,12884008,1722815,,12618455,17726680 17726680 6111556 </pubmed><br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/PMID PubMed]<br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=GuaB&diff=175822
GuaB
2012-09-06T08:10:01Z
<p>Antelmann: /* Extended information on the protein */</p>
<hr />
<div>* '''Description:''' IMP dehydrogenase <br/><br/><br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''guaB''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''guaA ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed] <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || IMP dehydrogenase<br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of GMP<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU00090 GuaB]<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/purine_biosynthesis.html Purine synthesis], [http://subtiwiki.uni-goettingen.de/pathways/gene_regulation_nucleotides.html Nucleotides (regulation)]'''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 6.168 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1464 bp, 488 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaC]]'', ''[[dacA]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11785&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:guaB_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=guaB_15915_17381_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:guaB_expression.png|500px]]<br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br />
<br />
<br/><br/><br/><br/><br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[biosynthesis/ acquisition of nucleotides]]}},<br />
{{SubtiWiki category|[[essential genes]]}},<br />
{{SubtiWiki category|[[phosphoproteins]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[CodY regulon]]}}<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU00090<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/guaB.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10073]<br />
<br />
=== Additional information===<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' Inosine 5'-phosphate + NAD<sup>+</sup> + H<sub>2</sub>O = xanthosine 5'-phosphate + NADH (according to Swiss-Prot) <br />
<br />
* '''Protein family:''' IMPDH/GMPR family (according to Swiss-Prot)<br />
<br />
* '''Paralogous protein(s):'''<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:''' <br />
** phosphorylated (STY) [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]<br />
** Cys308 is S-cysteinylated after diamide stress () [http://www.ncbi.nlm.nih.gov/pubmed/17611193 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]<br />
** Cys308 is S-bacillithiolated by NaOCl stress in B. subtilis and other Bacillus species [http://www.ncbi.nlm.nih.gov/pubmed/22938038 PubMed] <br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
** inhibition of enzymatic activity by (p)ppGpp during the ´stringent response´{{PubMed|6111556}}<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
<br />
* '''[[Localization]]:'''<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1VRD 1VRD] (from ''Thermotoga maritima msb8'', 60% identity, 80% similarity)<br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P21879 P21879]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00090]<br />
<br />
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.205 1.1.1.205]<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''guaB'' {{PubMed|22383849}} <br />
<br />
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=guaB_15915_17381_1 guaB] {{PubMed|22383849}}<br />
<br />
* '''Sigma factor:''' <br />
<br />
* '''Regulation:''' <br />
** activated during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]<br />
<br />
* '''Regulatory mechanism:''' <br />
** [[CodY]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]<br />
<br />
* '''Additional information:''' <br />
** the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]<br />
** inhibition of enzymatic activity by (p)ppGpp during the ´stringent response´{{PubMed|6111556}}<br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
** purification from ''B. subtilis'' with an N-terminal Strep-tag, for [[SPINE]], (in [[pGP380]]): pGP901, available in [[Stülke]] lab<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
<pubmed>17611193,12884008,1722815,,12618455,17726680 17726680 6111556 </pubmed><br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/PMID PubMed]<br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=GuaB&diff=175821
GuaB
2012-09-06T08:07:56Z
<p>Antelmann: /* Extended information on the protein */</p>
<hr />
<div>* '''Description:''' IMP dehydrogenase <br/><br/><br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''guaB''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''guaA ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed] <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || IMP dehydrogenase<br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of GMP<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU00090 GuaB]<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/purine_biosynthesis.html Purine synthesis], [http://subtiwiki.uni-goettingen.de/pathways/gene_regulation_nucleotides.html Nucleotides (regulation)]'''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 6.168 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1464 bp, 488 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaC]]'', ''[[dacA]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11785&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:guaB_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=guaB_15915_17381_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:guaB_expression.png|500px]]<br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br/><br/><br/><br/><br />
<br />
<br />
<br/><br/><br/><br/><br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[biosynthesis/ acquisition of nucleotides]]}},<br />
{{SubtiWiki category|[[essential genes]]}},<br />
{{SubtiWiki category|[[phosphoproteins]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[CodY regulon]]}}<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU00090<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/guaB.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10073]<br />
<br />
=== Additional information===<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' Inosine 5'-phosphate + NAD<sup>+</sup> + H<sub>2</sub>O = xanthosine 5'-phosphate + NADH (according to Swiss-Prot) <br />
<br />
* '''Protein family:''' IMPDH/GMPR family (according to Swiss-Prot)<br />
<br />
* '''Paralogous protein(s):'''<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:''' <br />
** phosphorylated (STY) [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]<br />
** S-cysteinlyation after diamide stress (Cys-308) [http://www.ncbi.nlm.nih.gov/pubmed/17611193 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]<br />
** S-bacillithiolated by NaOCl stress on Cys308-SSB in B. subtilis and other Bacillus species [http://www.ncbi.nlm.nih.gov/pubmed/22938038 PubMed] <br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
** inhibition of enzymatic activity by (p)ppGpp during the ´stringent response´{{PubMed|6111556}}<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
<br />
* '''[[Localization]]:'''<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1VRD 1VRD] (from ''Thermotoga maritima msb8'', 60% identity, 80% similarity)<br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P21879 P21879]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00090]<br />
<br />
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.205 1.1.1.205]<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''guaB'' {{PubMed|22383849}} <br />
<br />
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=guaB_15915_17381_1 guaB] {{PubMed|22383849}}<br />
<br />
* '''Sigma factor:''' <br />
<br />
* '''Regulation:''' <br />
** activated during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]<br />
<br />
* '''Regulatory mechanism:''' <br />
** [[CodY]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]<br />
<br />
* '''Additional information:''' <br />
** the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]<br />
** inhibition of enzymatic activity by (p)ppGpp during the ´stringent response´{{PubMed|6111556}}<br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
** purification from ''B. subtilis'' with an N-terminal Strep-tag, for [[SPINE]], (in [[pGP380]]): pGP901, available in [[Stülke]] lab<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
<pubmed>17611193,12884008,1722815,,12618455,17726680 17726680 6111556 </pubmed><br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/PMID PubMed]<br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=LutC&diff=154912
LutC
2012-03-22T09:09:30Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' lactate catabolic enzyme <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''lutC''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvbY ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || utilization of lactate<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26 kDa, 5.157 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 720 bp, 240 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvbX]]'', ''[[lutB]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15408&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:yvbY_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br/><br/><br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[utilization of specific carbon sources]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[LutR regulon]]}},<br />
{{SubtiWiki regulon|[[SinR regulon]]}}<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU34030<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
no growth with lactate as the single carbon source [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' no entry<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14091]<br />
<br />
=== Additional information===<br />
<br />
<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' oxidation of lactate to pyruvate [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]<br />
<br />
* '''Protein family:''' UPF0707 family (according to Swiss-Prot)<br />
<br />
* '''Paralogous protein(s):'''<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:'''<br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
<br />
* '''[[Localization]]:'''<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' <br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/O32259 O32259]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34030]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''[[lutA]]-[[lutB]]-[[lutC]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]<br />
<br />
* '''Sigma factor:''' <br />
<br />
* '''Regulation:''' induction by lactate [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]<br />
** repressed by [[SinR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]<br />
<br />
* '''Regulatory mechanism:''' dual repression by [[LutR]] (inducer lactate) and [[SinR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]<br />
** [[SinR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]<br />
<br />
* '''Additional information:''' <br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
[[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ homepage]<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
<pubmed>22427629,19201793, 19201793 </pubmed><br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=LutB&diff=154911
LutB
2012-03-22T09:07:54Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' lactate catabolic enzyme <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''lutB''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvfW ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || lactate oxidase<br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || lactate utilization<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 53 kDa, 5.848 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1437 bp, 479 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[lutC]]'', ''[[lutA]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15409&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:yvfW_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br/><br/><br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[utilization of specific carbon sources]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[FsrA regulon]]}},<br />
{{SubtiWiki regulon|[[LutR regulon]]}},<br />
{{SubtiWiki regulon|[[SinR regulon]]}}<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU34040<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
no growth with lactate as the single carbon source [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' no entry<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12448]<br />
<br />
=== Additional information===<br />
<br />
<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' oxidation of lactate to pyruvate [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]<br />
<br />
* '''Protein family:'''<br />
<br />
* '''Paralogous protein(s):'''<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:'''<br />
<br />
* '''Cofactor(s):''' contains an iron-sulfur cluster<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
<br />
* '''[[Localization]]:'''<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' <br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/O07021 O07021]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34040]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''[[lutA]]-[[lutB]]-[[lutC]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]<br />
<br />
* '''[[Sigma factor]]:''' <br />
<br />
* '''Regulation:''' <br />
** repressed by [[SinR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]<br />
** induction by lactate [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]<br />
** less expressed under conditions of extreme iron limitation ([[FsrA]]) [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]<br />
** part of the iron sparing response ([[FsrA]]) {{PubMed|22389480}}<br />
<br />
* '''Regulatory mechanism:''' <br />
** [[SinR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]<br />
** dual repression by [[LutR]] (inducer lactate) and [[SinR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]<br />
** [[FsrA]]: translational repression {{PubMed|18697947}} <br />
<br />
* '''Additional information:'''<br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
[[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ homepage]<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
<pubmed>22427629,18697947,16430695,22389480,19201793, 19201793 </pubmed><br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=LutA&diff=154910
LutA
2012-03-22T09:06:34Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' lactate catabolic enzyme <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''lutA''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvfV''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || lactate oxidase<br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || lactate utilization<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26 kDa, 6.25 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 714 bp, 238 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[lutB]]'', ''[[yvfU]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15410&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:yvfV_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br/><br/><br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[utilization of specific carbon sources]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[LutR regulon]]}},<br />
{{SubtiWiki regulon|[[SinR regulon]]}}<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU34050<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
no growth with lactate as the single carbon source [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' no entry<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12447]<br />
<br />
=== Additional information===<br />
<br />
<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' oxidation of lactate to pyruvate [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]<br />
<br />
* '''Protein family:'''<br />
<br />
* '''Paralogous protein(s):'''<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:'''<br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
<br />
* '''[[Localization]]:'''<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' <br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/O07020 O07020]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU34050]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''[[lutA]]-[[lutB]]-[[lutC]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]<br />
<br />
* '''Sigma factor:''' <br />
<br />
* '''Regulation:''' induction by lactate [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]<br />
** repressed by [[SinR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]<br />
<br />
* '''Regulatory mechanism:''' dual repression by [[LutR]] (inducer lactate) and [[SinR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]<br />
** [[SinR]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/19201793 PubMed]<br />
<br />
* '''Additional information:''' <br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
[[Richard Losick]], Harvard Univ., Cambridge, USA [http://www.mcb.harvard.edu/Losick/ homepage]<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
<pubmed>22427629,16430695,19201793, 19201793 </pubmed><br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=FsrA&diff=154909
FsrA
2012-03-22T09:04:54Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' regulatory RNA<br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''fsrA''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || sRNA FsrA<br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || inhibition of ''[[sdhC]]'' translation<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length''' || aaa bp<br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykuI]]'', ''[[ykuJ]]''<br />
|-<br />
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE_nucleotide.txt Gene sequence (+200bp) ]''' <br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:FsrA_context.jpg]]<br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[carbon core metabolism]]}},<br />
{{SubtiWiki category|[[ncRNA]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[Fur regulon]]}}<br />
=The [[FsrA regulon]]''=<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:'''<br />
<br />
===Phenotypes of a mutant ===<br />
* transcription profile of a ''[[fsrA]]'' mutant strain: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27416 GEO] {{PubMed|22389480}}<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' no entry<br />
<br />
* '''SubtiList entry:''' no entry<br />
<br />
* '''GEO entry:''' [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27416 GEO] {{PubMed|22389480}}<br />
<br />
* '''Structure:'''<br />
<br />
=== Additional information===<br />
<br />
* '''Swiss prot entry:'''<br />
<br />
* '''KEGG entry:''' no entry<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
<br />
<br />
=The RNA=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' hybridizes to ''[[sdhC]], [[citB]], [[lutB]], [[gltA]]-[[gltB]]'', and ''[[leuC]]-[[leuD]]'' mRNAs and inhibits their translation. {{PubMed|18697947,22389480}}<br />
<br />
=== Extended information on the RNA===<br />
<br />
* '''Kinetic information''' <br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
** Binds ''[[sdhC]], [[citB]], [[lutB]], [[gltA]]-[[gltB]]'', and ''[[leuC]]-[[leuD]]'' mRNAs {{PubMed|18697947,22389480}}<br />
<br />
* '''[[Localization]]'''<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure''': <br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' <br />
<br />
* '''[[Sigma factor]]:''' <br />
<br />
* '''Regulation:''' induced by iron starvation ([[Fur]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/18697947 PubMed]<br />
<br />
* '''Regulatory mechanism:''' [[Fur]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/18697947 PubMed]<br />
<br />
* '''Additional information:'''<br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
=Labs working on this gene/RNA=<br />
<br />
[[John Helmann]], Cornell University, USA [http://www.micro.cornell.edu/research/labs/helmann-lab/index.cfm Homepage]<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
<pubmed>22427629,18697947,22389480</pubmed><br />
<br />
[[Category:small RNA]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=GapA&diff=154827
GapA
2012-03-14T15:12:10Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' Glyceraldehyde 3-phosphate dehydrogenase, NAD-dependent, glycolytic enzyme <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''gapA''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || Yes [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 (PubMed)]<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || glyceraldehyde 3-phosphate dehydrogenase<br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || catabolic enzyme in glycolysis<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/GapA GapA]<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 35.7 kDa, 5.03<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1005 bp, 335 amino acids<br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pgk]]'', ''[[cggR]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15399&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:gapA_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br/><br/><br/><br/><br />
<br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[carbon core metabolism]]}},<br />
{{SubtiWiki category|[[membrane proteins]]}},<br />
{{SubtiWiki category|[[phosphoproteins]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[CggR regulon]]}}<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU33940<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
* Essential [http://www.ncbi.nlm.nih.gov/pubmed/17114254 PubMed]<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]<br />
<br />
* '''SubtiList entry:'''[http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10827]<br />
<br />
=== Additional information===<br />
<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' D-glyceraldehyde 3-phosphate + phosphate + NAD<sup>+</sup> = 3-phospho-D-glyceroyl phosphate + NADH (according to Swiss-Prot)<br />
** This reaction is part of the glycolysis.<br />
<br />
* '''Protein family:''' glyceraldehyde-3-phosphate dehydrogenase family (according to Swiss-Prot)<br />
<br />
* '''Paralogous protein(s):''' [[GapB]]<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' Michaelis-Menten [http://www.ncbi.nlm.nih.gov/sites/entrez/10799476 PubMed] <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:''' <br />
** Phosphorylation on (Ser-148 OR Ser-151 OR Thr-153 OR Thr-154) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed1], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed2]<br />
** Reversible thiol modifications after exposure to toxic quinones [http://www.ncbi.nlm.nih.gov/sites/entrez/18673455 PubMed]<br />
** Cys152-Cys156 form intramolecular disulfide in response to disulfide stress (diamide, NaOCl-stress) [http://www.ncbi.nlm.nih.gov/sites/entrez/21749987 PubMed]<br />
<br />
* '''Cofactor(s):''' NAD+ (do not accept NADP+) [http://www.ncbi.nlm.nih.gov/sites/entrez/10799476 PubMed]<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
** [[GapA]]-[[PtsH]]: [[PtsH|HPr(Ser-46-P)]] binds GapA resulting in a slight inhibition of enzymatic activity [http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed]<br />
** [[GapA]]-[[Crh]]: [[Crh|Crh(Ser-46-P)]] binds GapA resulting in a slight inhibition of enzymatic activity.[http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed]<br />
** [[GapA]]-[[YkzW]] {{PubMed|20444087}}<br />
<br />
* '''[[Localization]]:''' <br />
** cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/14600241 PubMed]<br />
** loosely membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' <br />
** [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1GD1 1GD1] (from ''Geobacillus stearothermophilus'')<br />
** [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NQO 1NQO] (from ''Geobacillus stearothermophilus'', mutant with cys 149 replaced by ser, complex with NAD+ und D-Glyceraldehyde-3-Phosphate) <br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P09124 P09124]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33940]<br />
<br />
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.2.1.12 1.2.1.12]<br />
<br />
=== Additional information===<br />
* GAP dehydrogenases from different sources (incl. ''Geobacillus stearothermophilus'') were shown to cleave RNA ([http://www.ncbi.nlm.nih.gov/sites/entrez/12359717 PubMed])<br />
* Moreover, mutations in ''gapA'' from ''B. subtilis'' can suppress mutations in genes involved in DNA replication ([http://www.ncbi.nlm.nih.gov/sites/entrez/17505547 PubMed]).<br />
* extensive information on the structure and enzymatic properties of GapA can be found at [http://www.proteopedia.org/wiki/index.php/Glyceraldehyde-3-Phosphate_Dehydrogenase Proteopedia]<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' <br />
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpi]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}} <br />
** ''[[cggR]]-[[gapA]]'' {{PubMed|11489127}} <br />
<br />
* '''Sigma factor:''' [[SigA]] {{PubMed|11489127}} <br />
<br />
* '''Regulation:''' <br />
** expression activated by glucose (10 fold) ([[CggR]]) {{PubMed|12850135,12622823}} <br />
<br />
* '''Regulatory mechanism:''' <br />
** [[CggR]]: transcription repression {{PubMed|11489127}} <br />
<br />
* '''Database entries:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html DBTBS]<br />
<br />
* '''Additional information:''' <br />
** GapA is one of the most abundant proteins in the cell. In the presence of glucose, there are about 25,000 GapA molecules per cell ([http://www.ncbi.nlm.nih.gov/sites/entrez/12634343 PubMed]).<br />
** The primary mRNAs of the operon are highly unstable. The primary mRNA is subject to processing at the very end of the ''[[cggR]]'' open reading frame. This results in stable mature ''[[gapA]]'' and ''[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' mRNAs. {{PubMed|11489127}} The processing event requires the [[Rny|RNase Y]] {{PubMed|19193632}}.<br />
** The accumulation of the ''[[cggR]]-[[gapA]]'' mRNA is strongly dependent on the presence of the [[YkzW]] peptide, due to stabilization of the mRNA {{PubMed|20444087}}.<br />
** the mRNA is substantially stabilized upon depletion of [[Rny|RNase Y]] {{PubMed|21815947}}<br />
<br />
=Biological materials =<br />
* '''Mutant:'''<br />
** GP592 (''gapA''::''cat''), available in [[Stülke]] lab<br />
** GP597 (''gapA''::''erm''), available in [[Stülke]] lab<br />
** GP703 (''gapA''::''cat'' ''gapB''::''spec''), available in [[Stülke]] lab<br />
** GM1501 (under p(spac) control), available in [[Stephane Aymerich]] lab<br />
<br />
* '''Expression vector:''' <br />
** pGP1424 (expression in ''B. subtilis'', in [[pBQ200]]) (available in [[Stülke]] lab)<br />
** pGP90 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)<br />
** pGP704 (N-terminal His-tag, in [[pWH844]]) (available in [[Stülke]] lab)<br />
<br />
* '''lacZ fusion:''' pGP506 (in [[pAC7]]), pGP512 (in [[pAC6]]) (available in [[Stülke]] lab)<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab<br />
<br />
* '''Antibody:''' available in [[Stülke]] lab<br />
<br />
=Labs working on this gene/protein=<br />
<br />
[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France<br />
<br />
[[Stülke|Jörg Stülke]], University of Göttingen, Germany<br />
[http://wwwuser.gwdg.de/~genmibio/stuelke.html homepage]<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<big>''Lehnik-Habrink M, Schaffer M, Mäder U, Diethmaier C, Herzberg C, Stülke J'' </big><br />
<big>'''RNA processing in ''Bacillus subtilis'': identification of targets of the essential RNase Y.''' </big><br />
<big>Mol Microbiol. 2011 81(6): 1459-1473. </big><br />
[http://www.ncbi.nlm.nih.gov/pubmed/21815947 PubMed:21815947]<br />
<pubmed> 21749987,12850135,19193632, 18673455 , 20444087 17726680,16479537,12622823, 12359717,10799476,17505547,11489127, 12123463,17218307, 12634343, 17142398, 17114254,10559165 </pubmed><br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=OhrB&diff=154826
OhrB
2012-03-14T15:05:23Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' general stress protein <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''ohrB ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yzzE, ykzA ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || organic peroxide resistance<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 14 kDa, 4.735 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 408 bp, 136 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ohrR]]'', ''[[guaD]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13173&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:ykzA_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[general stress proteins (controlled by SigB)]]}},<br />
{{SubtiWiki category|[[resistance against oxidative and electrophile stress]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[SigB regulon]]}}<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU13160<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ohrB.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG19021]<br />
<br />
=== Additional information===<br />
<br />
<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' <br />
<br />
* '''Protein family:''' osmC/ohr family (according to Swiss-Prot)<br />
<br />
* '''Paralogous protein(s):'''<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:'''Cys55-Cys119 form catalytic disulfide bond <br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
<br />
* '''[[Localization]]:'''<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2BJO 2BJO] <br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P80242 P80242]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU13160]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
:* subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''ohrB'' {{PubMed|9696771}} <br />
<br />
* '''[[Sigma factor]]:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed] <br />
<br />
* '''Regulation:''' <br />
** induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]<br />
<br />
* '''Regulatory mechanism:''' <br />
<br />
* '''Additional information:''' <br />
** subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed] <br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
<pubmed>18084074,9696771,11418552 ,15805528, </pubmed><br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=FsrA&diff=154757
FsrA
2012-03-07T09:10:15Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' regulatory RNA<br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''fsrA''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || sRNA FsrA<br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || inhibition of ''[[sdhC]]'' translation<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length''' || aaa bp<br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykuI]]'', ''[[ykuJ]]''<br />
|-<br />
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE_nucleotide.txt Gene sequence (+200bp) ]''' <br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:FsrA_context.jpg]]<br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[carbon core metabolism]]}},<br />
{{SubtiWiki category|[[ncRNA]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[Fur regulon]]}}<br />
=The [[FsrA regulon]]: ''[[citB]]'', ''[[leuC]]-[[leuD]]'', ''[[lutB]]'', ''[[sdhC]]''=<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:'''<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' no entry<br />
<br />
* '''SubtiList entry:''' no entry<br />
<br />
* '''Structure:''' <br />
<br />
=== Additional information===<br />
<br />
* '''Swiss prot entry:'''<br />
<br />
* '''KEGG entry:''' no entry<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
<br />
<br />
=The RNA=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' hybridizes to ''[[sdhC]], [[citB]], [[lutB]], and [[leuC]]-[[leuD]]'' mRNAs and inhibits their translation. [http://www.ncbi.nlm.nih.gov/sites/entrez/18697947 PubMed]<br />
<br />
=== Extended information on the RNA===<br />
<br />
* '''Kinetic information''' <br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
** Binds ''[[sdhC]], [[citB]], [[lutB]], and [[leuC]]-[[leuD]]'' mRNAs [http://www.ncbi.nlm.nih.gov/sites/entrez/18697947 PubMed]<br />
<br />
* '''[[Localization]]'''<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure''': <br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' <br />
<br />
* '''[[Sigma factor]]:''' <br />
<br />
* '''Regulation:''' induced by iron starvation ([[Fur]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/18697947 PubMed]<br />
<br />
* '''Regulatory mechanism:''' [[Fur]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/18697947 PubMed]<br />
<br />
* '''Additional information:'''<br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
=Labs working on this gene/RNA=<br />
<br />
[[John Helmann]], Cornell University, USA [http://www.micro.cornell.edu/research/labs/helmann-lab/index.cfm Homepage]<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
<pubmed>18697947,22389480</pubmed><br />
<br />
[[Category:small RNA]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=AdhR&diff=148481
AdhR
2012-01-16T20:29:04Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' MerR/NmlR-family transcriptional activator of ''[[adhA]]-[[yraA]]'', responsive to formaldehyde and methylglyoxal <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''adhR ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yraB''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || MerR/NmlR-family transcriptional activator <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of the protective response to formaldehyde and methylglyoxal<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 16 kDa, 9.637 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 420 bp, 140 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yraD]]'', ''[[adhA]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14642&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|-<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:yraB_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[transcription factors and their control]]}},<br />
{{SubtiWiki category|[[resistance against oxidative and electrophile stress]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU27000<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' no entry<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13777]<br />
<br />
=== Additional information===<br />
<br />
<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' <br />
<br />
* '''Protein family:'''MerR/NmlR-family of regulators <br />
<br />
* '''Paralogous protein(s):'''<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:''' activity probably redox-controlled via thiol-(S)-alkylation at Cys-52 by aldehydes {{PubMed|19170879}}<br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
<br />
* '''[[Localization]]:''' cytoplasmic<br />
=== Database entries ===<br />
<br />
* '''Structure:''' <br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/O06008 O06008]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU27000]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' <br />
<br />
* '''[[Sigma factor]]:''' <br />
<br />
* '''Regulation:'''<br />
<br />
* '''Regulatory mechanism:''' <br />
<br />
* '''Additional information:''' <br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
[[Haike Antelmann]],University of Greifswald, Germany<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
=Reviews=<br />
<br />
<pubmed>21722790</pubmed><br />
<br />
Antelmann H, Helmann JD.<br />
Thiol-based redox switches and gene regulation.<br />
Antioxid Redox Signal. 2011,14:1049-63. <br />
<br />
=Original articles=<br />
<br />
<pubmed>19170879</pubmed><br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=HypO&diff=148480
HypO
2012-01-16T20:08:45Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' NAD(P)H-flavin nitroreductase <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''hypO''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yfkO''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || NAD(P)H-flavin nitroreductase <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || probably involved in NaOCl and diamide detoxification<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 25 kDa, 5.667 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 663 bp, 221 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[treR]]'', ''[[yfkN]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12612&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:yfkO_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[electron transport/ other]]}},<br />
{{SubtiWiki category|[[resistance against oxidative and electrophile stress]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[HypR regulon]]}}<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU07830<br />
<br />
===Phenotypes of a mutant ===<br />
* a ''[[hypO]] [[ohrA]]'' mutant is more sensitive to NaOCl stress than ''[[ohrA]]'' single mutant {{PubMed|22238377}}<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yfkO.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12931]<br />
<br />
=== Additional information===<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' <br />
<br />
* '''Protein family:''' nitroreductase family (according to Swiss-Prot)<br />
<br />
* '''Paralogous protein(s):'''<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:'''<br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
<br />
* '''[[Localization]]:'''<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' <br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/O34475 O34475]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU07830]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''hypO'' (according to [http://dbtbs.hgc.jp/COG/prom/yfkO.html DBTBS])<br />
<br />
* '''[[Sigma factor]]:''' <br />
<br />
* '''Regulation:''' <br />
** induced under disulfide stress conditions (diamide, NaOCl) ([[HypR]]) {{PubMed|22238377}} <br />
<br />
* '''Regulatory mechanism:''' <br />
** [[HypR]]:transcription activation {{PubMed|22238377}} <br />
<br />
* '''Additional information:'''<br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
* [[Haike Antelmann]], University of Greifswald, Germany<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
==Original articles==<br />
<pubmed>20727918</pubmed><br />
<br />
Palm GJ, Khanh Chi B, Waack P, Gronau K, Becher D, Albrecht D, Hinrichs W, Read RJ, Antelmann H.<br />
Structural insights into the redox-switch mechanism of the MarR/DUF24-type regulator HypR.<br />
Nucleic Acids Res. 2012, Jan 11. [Epub ahead of print]<br />
{{PubMed|22238377}}<br />
<br />
<br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=OhrR&diff=148479
OhrR
2012-01-16T20:06:31Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' transcription repressor of the ''[[ohrA]]'' gene <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''ohrR ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykmA''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || transcription repressor (MarR family) <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of ''[[ohrA]]'' expression <br/>in response to organic peroxides<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 16 kDa, 6.364 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 441 bp, 147 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ohrA]]'', ''[[ohrB]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13172&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:ykmA_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[transcription factors and their control]]}},<br />
{{SubtiWiki category|[[resistance against oxidative and electrophile stress]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
<br />
=The [[OhrR regulon]]:=<br />
* ''[[ohrA]]''<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU13150<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ykmA.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13239]<br />
<br />
=== Additional information===<br />
<br />
<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' <br />
<br />
* '''Protein family:'''<br />
<br />
* '''Paralogous protein(s):'''<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:''' <br />
** senses organic peroxides, released from DNA upon oxidation of an active site cysteine<br />
** S-bacillithiolation upon hypochlorite stress on Cys-15, this results in release from the'' [[ohrA]]'' promoter {{PubMed|21749987}} <br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
** forms dimers<br />
<br />
* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot)<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1Z91 1Z91] (reduced form), [http://www.rcsb.org/pdb/explore.do?structureId=1Z9C 1Z9C] (complex with ''[[ohrA]]'' promoter) <br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/O34777 O34777]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU13150]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''ohrR'' {{PubMed|9696771}}<br />
<br />
* '''[[Sigma factor]]:''' [[SigA]] <br />
<br />
* '''Regulation:''' <br />
<br />
* '''Regulatory mechanism:''' <br />
<br />
* '''Additional information:''' <br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
[[John Helmann]], Cornell University, USA [http://www.micro.cornell.edu/research/labs/helmann-lab/index.cfm Homepage]<br />
<br />
[[Richard Brennan]], Houston, Texas, USA [http://www.mdanderson.org/departments/biochem/display.cfm?id=556ef368-6c81-4043-b74f350d41dd06cb&method=displayfull&pn=a8427ebd-d0ff-11d4-80fd00508b603a14 Homepage]<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
==Reviews==<br />
Antelmann H, Helmann JD.<br />
Thiol-based redox switches and gene regulation.<br />
Antioxid Redox Signal. 2011,14:1049-63.<br />
{{PubMed|20626317}}<br />
<br />
<pubmed>19575568 20094649 </pubmed><br />
<br />
==Original Publications==<br />
<pubmed>16209951,18487332,17660290,17502599,12486061,11418552,18586944,11983871,18363800,19129220 9696771 21749987 </pubmed><br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=CatR&diff=148478
CatR
2012-01-16T20:02:05Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' MarR/DUF24-family transcription repressor of the ''[[catD]]-[[catE]]'' operon <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''catR''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvaP''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || MarR/DUF24-family transcription repressor <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || Resistance against oxidative and electrophile stress<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26 kDa, 9.887 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 708 bp, 236 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvaO]]'', ''[[yvaQ]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15373&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:yvaP_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[transcription factors and their control]]}},<br />
{{SubtiWiki category|[[resistance against oxidative and electrophile stress]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
<br />
=The [[CatR regulon]]:=<br />
''[[catD]]-[[catE]]''<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU33680<br />
<br />
===Phenotypes of a mutant ===<br />
increased resistance to catechol and quinones {{PubMed|20639328}} <br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' no entry<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14071]<br />
<br />
=== Additional information===<br />
<br />
<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' MarR/DUF24-family transcription repressor of the'' [[catD]]-[[catE]]'' operon {{PubMed|20639328}} <br />
<br />
* '''Protein family:'''<br />
<br />
* '''Paralogous protein(s):''' [[YodB]]<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:''' in responsse to the presence of diamides or quinones, Cys-7 forms intermolecular disulfide bonds, this results in loss of DNA-bindig ability (induction of ''[[catD]]-[[catE]]'') {{PubMed|20639328}} <br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
<br />
* '''[[Localization]]:'''<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' <br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/O32238 O32238]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33680]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' <br />
<br />
* '''[[Sigma factor]]:''' <br />
<br />
* '''Regulation:''' <br />
<br />
* '''Regulatory mechanism:''' <br />
<br />
* '''Additional information:''' <br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
[[Haike Antelmann]],University of Greifswald, Germany<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
=Reviews=<br />
<br />
Antelmann H, Helmann JD.<br />
Thiol-based redox switches and gene regulation.<br />
Antioxid Redox Signal. 2011,14:1049-63.<br />
{{PubMed|20626317}}<br />
<br />
<pubmed>18282125</pubmed><br />
<br />
=Original Articles=<br />
<br />
<pubmed> 20639328 </pubmed><br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=MhqR&diff=148477
MhqR
2012-01-16T20:00:53Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' MarR-family transcriptional repressor of ''[[azoR2]]'', ''[[mhqA]]'', ''[[mhqD]]-[[mhqE]]'' and ''[[mhqN]]-[[mhqO]]-[[mhqP]]'' expression <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''mhqR ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykvE''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || MarR-family transcriptional repressor<br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of resistance to quinones and diamide<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 16 kDa, 6.42 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 435 bp, 145 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[kinD]]'', ''[[motB]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13240&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:ykvE_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[transcription factors and their control]]}},<br />
{{SubtiWiki category|[[resistance against oxidative and electrophile stress]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
<br />
=The [[MhqR regulon]]=<br />
<br />
* ''[[azoR2]]'', ''[[mhqA]]'', ''[[mhqD]]-[[mhqE]]'' and ''[[mhqN]]-[[mhqO]]-[[mhqP]]'' <br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU13670<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
* '''resistant to quinones and diamide''' <br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' no entry<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13310]<br />
<br />
=== Additional information===<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' <br />
<br />
* '''Protein family:'''<br />
<br />
* '''Paralogous protein(s):'''<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:'''<br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
<br />
* '''[[Localization]]:'''<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' <br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/O31672 O31672]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU13670]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
* '''Binding site:''' tATCTcgaAtTCgAGATaaaa {{PubMed|17725564}} <br />
=Expression and regulation=<br />
<br />
* '''Operon:''' <br />
<br />
* '''[[Sigma factor]]:''' <br />
<br />
* '''Regulation:''' <br />
<br />
* '''Regulatory mechanism:''' <br />
<br />
* '''Additional information:''' <br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
[[Haike Antelmann]],University of Greifswald, Germany<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
=Reviews=<br />
<br />
<pubmed>18282125</pubmed><br />
<br />
=Original articles=<br />
<br />
<pubmed>17725564,, </pubmed><br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=CatR&diff=148476
CatR
2012-01-16T19:58:44Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' MarR/DUF24-family transcription repressor of the ''[[catD]]-[[catE]]'' operon <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''yvaP''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || MarR/DUF24-family transcription repressor <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || Resistance against oxidative and electrophile stress<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26 kDa, 9.887 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 708 bp, 236 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvaO]]'', ''[[yvaQ]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15373&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:yvaP_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[transcription factors and their control]]}},<br />
{{SubtiWiki category|[[resistance against oxidative and electrophile stress]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
<br />
=The [[CatR regulon]]:=<br />
''[[catD]]-[[catE]]''<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU33680<br />
<br />
===Phenotypes of a mutant ===<br />
increased resistance to catechol and quinones {{PubMed|20639328}} <br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' no entry<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14071]<br />
<br />
=== Additional information===<br />
<br />
<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' MarR/DUF24-family transcription repressor of the'' [[catD]]-[[catE]]'' operon {{PubMed|20639328}} <br />
<br />
* '''Protein family:'''<br />
<br />
* '''Paralogous protein(s):''' [[YodB]]<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:''' in responsse to the presence of diamides or quinones, Cys-7 forms intermolecular disulfide bonds, this results in loss of DNA-bindig ability (induction of ''[[catD]]-[[catE]]'') {{PubMed|20639328}} <br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
<br />
* '''[[Localization]]:'''<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' <br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/O32238 O32238]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33680]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' <br />
<br />
* '''[[Sigma factor]]:''' <br />
<br />
* '''Regulation:''' <br />
<br />
* '''Regulatory mechanism:''' <br />
<br />
* '''Additional information:''' <br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
[[Haike Antelmann]],University of Greifswald, Germany<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
=Reviews=<br />
<br />
Antelmann H, Helmann JD.<br />
Thiol-based redox switches and gene regulation.<br />
Antioxid Redox Signal. 2011,14:1049-63.<br />
{{PubMed|20626317}}<br />
<br />
<pubmed>18282125</pubmed><br />
<br />
=Original Articles=<br />
<br />
<pubmed> 20639328 </pubmed><br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=YodB&diff=148475
YodB
2012-01-16T19:56:15Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' MarR/DUF24-family transcription repressor of ''[[azoR1]]'', ''[[catD]]-[[catE]]'' and ''[[yodC]]'' expression <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''yodB''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || MarR/DUF24-family transcription repressor <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of quinone and diamide detoxification<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 12 kDa, 4.737 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 336 bp, 112 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yodA]]'', ''[[yodC]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13845&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:yodB_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[transcription factors and their control]]}},<br />
{{SubtiWiki category|[[resistance against oxidative and electrophile stress]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[YodB regulon]]}}<br />
<br />
=The [[YodB regulon]]:=<br />
* ''[[azoR1]]'', ''[[catD]]-[[catE]]'', ''[[yodB]]'', ''[[yodC]]''<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU19540<br />
<br />
===Phenotypes of a mutant ===<br />
increased resistance to catechol, quinones and diamide {{PubMed|20639328}} <br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' no entry<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13531]<br />
<br />
=== Additional information===<br />
<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' <br />
<br />
* '''Protein family:''' MarR/DUF24-family <br />
<br />
* '''Paralogous protein(s):''' [[CatR]]<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:''' redox-controlled by intersubunit disulfide formation of Cys6 and Cys101' in response to quinones and diamide<br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''[[SubtInteract|Interactions]]:''' <br />
<br />
* '''[[Localization]]:'''<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' <br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/O34844 O34844]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU19540]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' <br />
<br />
* '''[[Sigma factor]]:''' <br />
<br />
* '''Regulation:''' <br />
** subject to autorepression {{PubMed|21749987}} <br />
<br />
* '''Regulatory mechanism:''' <br />
** YodB: transcription repression {{PubMed|21749987}} <br />
<br />
* '''Additional information:''' <br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
[[Haike Antelmann]],University of Greifswald, Germany<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
==Reviews==<br />
<br />
Antelmann H, Helmann JD.<br />
Thiol-based redox switches and gene regulation.<br />
Antioxid Redox Signal. 2011,14:1049-63.<br />
{{PubMed|20626317}}<br />
<br />
<pubmed>18282125</pubmed><br />
<br />
==Original Publications==<br />
<pubmed>17158660,17407181,18208493,20639328,20652907,21749987</pubmed><br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=HypO&diff=148474
HypO
2012-01-16T19:53:09Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' NAD(P)H-flavin nitroreductase <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''hypO''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yfkO''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || NAD(P)H-flavin nitroreductase <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || probably involved in NaOCl and diamide detoxification<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 25 kDa, 5.667 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 663 bp, 221 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[treR]]'', ''[[yfkN]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12612&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:yfkO_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[electron transport/ other]]}},<br />
{{SubtiWiki category|[[resistance against oxidative and electrophile stress]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[HypR regulon]]}}<br />
<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU07830<br />
<br />
===Phenotypes of a mutant ===<br />
* a ''[[hypO]] [[ohrA]]'' mutant is more sensitive to NaOCl stress than ''[[ohrA]]'' single mutant {{PubMed|22238377}}<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yfkO.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12931]<br />
<br />
=== Additional information===<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' <br />
<br />
* '''Protein family:''' nitroreductase family (according to Swiss-Prot)<br />
<br />
* '''Paralogous protein(s):'''<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:'''<br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
<br />
* '''[[Localization]]:'''<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' <br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/O34475 O34475]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU07830]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''hypO'' (according to [http://dbtbs.hgc.jp/COG/prom/yfkO.html DBTBS])<br />
<br />
* '''[[Sigma factor]]:''' <br />
<br />
* '''Regulation:''' <br />
** induced under disulfide stress conditions (diamide, NaOCl) ([[HypR]]) {{PubMed|22238377}} <br />
<br />
* '''Regulatory mechanism:''' <br />
** [[HypR]]:transcription activation {{PubMed|22238377}} <br />
<br />
* '''Additional information:'''<br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
* Haike Antelmann, University of Greifswald, Germany<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
==Original articles==<br />
<pubmed>20727918</pubmed><br />
<br />
Palm GJ, Khanh Chi B, Waack P, Gronau K, Becher D, Albrecht D, Hinrichs W, Read RJ, Antelmann H.<br />
Structural insights into the redox-switch mechanism of the MarR/DUF24-type regulator HypR.<br />
Nucleic Acids Res. 2012, Jan 11. [Epub ahead of print]<br />
{{PubMed|22238377}}<br />
<br />
<br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=HypO&diff=148473
HypO
2012-01-16T19:51:51Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' NAD(P)H-flavin nitroreductase <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''hypO''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yfkO''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || NAD(P)H-flavin nitroreductase <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || probably involved in NaOCl and diamide detoxification<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 25 kDa, 5.667 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 663 bp, 221 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[treR]]'', ''[[yfkN]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12612&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:yfkO_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[electron transport/ other]]}},<br />
{{SubtiWiki category|[[resistance against oxidative and electrophile stress]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[HypR regulon]]}}<br />
<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU07830<br />
<br />
===Phenotypes of a mutant ===<br />
* a ''[[hypO]] [[ohrA]]'' mutant is more sensitive to NaOCl stress than ''[[ohrA]]'' single mutant {{PubMed|22238377}}<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yfkO.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12931]<br />
<br />
=== Additional information===<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' <br />
<br />
* '''Protein family:''' nitroreductase family (according to Swiss-Prot)<br />
<br />
* '''Paralogous protein(s):'''<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:'''<br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
<br />
* '''[[Localization]]:'''<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' <br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/O34475 O34475]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU07830]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''hypO'' (according to [http://dbtbs.hgc.jp/COG/prom/yfkO.html DBTBS])<br />
<br />
* '''[[Sigma factor]]:''' <br />
<br />
* '''Regulation:''' <br />
** induced under disulfide stress conditions (diamide, NaOCl) ([[HypR]]) {{PubMed|22238377}} <br />
<br />
* '''Regulatory mechanism:''' <br />
** [[HypR]]:transcription activation {{PubMed|22238377}} <br />
<br />
* '''Additional information:'''<br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
==Original articles==<br />
<pubmed>20727918</pubmed><br />
<br />
Palm GJ, Khanh Chi B, Waack P, Gronau K, Becher D, Albrecht D, Hinrichs W, Read RJ, Antelmann H.<br />
Structural insights into the redox-switch mechanism of the MarR/DUF24-type regulator HypR.<br />
Nucleic Acids Res. 2012, Jan 11. [Epub ahead of print]<br />
{{PubMed|22238377}}<br />
<br />
<br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=HypR&diff=148472
HypR
2012-01-16T19:49:53Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' MarR/DUF24-family transcription regulator, positively controls the nitroreductase gene ''[[hypO]]'' in response to disulfide stress <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
| ''hypR'' <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yybR''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || MarR/DUF24-family transcription regulator HypR <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || control of the nitroreductase gene ''[[hypO]]'' in response to disulfide stress (diamide, NaOCl)<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 14 kDa, 8.415 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 375 bp, 125 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cotF]]'', ''[[ppaC]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16091&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:yybR_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[transcription factors and their control]]}},<br />
{{SubtiWiki category|[[resistance against oxidative and electrophile stress]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[HypR regulon]]}}<br />
<br />
= The [[HypR regulon]]:=<br />
* ''[[hypR]]'', ''[[hypO]]'' <br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU40540<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yybR.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10013]<br />
<br />
=== Additional information===<br />
''hypR'' is autoregulated by disulfide stress<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' <br />
<br />
* '''Protein family:''' MarR/DUF24-family regulator<br />
<br />
* '''Paralogous protein(s):''' [[YdeP]],[[YkvN]]<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' Cys14 redox sensing Cys, has lower pKa of 6.36 {{PubMed|22238377}} <br />
<br />
* '''Domains:''' <br />
** 5 alpha helices, 2 beta sheets, MarR-fold with wHTH motif, alpha4 major groove recognition helix, beta2 and 3 form the wing; alpha5 dimer interface {{PubMed|22238377}} <br />
<br />
* '''Modification:''' <br />
** oxidized to Cys14-Cys49' intersubunit disulfides by disulfide stress {{PubMed|22238377}} <br />
** Cys14 and Cys49' are about 8-9 Angström apart in reduced HypR-Dimer, oxidation moves the major groove recognition alpha4 helices of the HypR dimer about 4 Angstroem towards each other that leads to activation of HypR {{PubMed|22238377}} <br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
<br />
* '''[[Localization]]:'''<br />
** cytoplasmic<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' <br />
** reduced HypRC14S dimer [http://www.pdb.org/pdb/explore.do?structureId=4A5N] {{PubMed|22238377}} <br />
** oxidized HypR C14-C49' intersubunit disulfide-linked dimer [http://www.pdb.org/pdb/explore.do?structureId=4A5M] {{PubMed|22238377}} <br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P37486 P37486]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40540]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''hypR'' (according to [http://dbtbs.hgc.jp/COG/prom/yybR.html DBTBS])<br />
<br />
* '''[[Sigma factor]]:''' <br />
<br />
* '''Regulation:''' <br />
** activated by disulfide stress conditions (diamide, NaOCl) ''in vivo'' and ''in vitro '' {{PubMed|22238377}} <br />
<br />
* '''Regulatory mechanism:'''<br />
** redox-controlled by Cys14-Cys49' intersubunit disulfide formation by diamide and NaOCl ''in vitro'' and ''in vivo'' {{PubMed|22238377}} <br />
<br />
* '''Additional information:''' <br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
* [[Haike Antelmann]],University of Greifswald, Germany<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
==Reviews==<br />
<br />
Antelmann H, Helmann JD.<br />
Thiol-based redox switches and gene regulation.<br />
Antioxid Redox Signal. 2011,14:1049-63.<br />
{{PubMed|20626317}}<br />
<br />
==Original articles==<br />
<br />
Palm GJ, Khanh Chi B, Waack P, Gronau K, Becher D, Albrecht D, Hinrichs W, Read RJ, Antelmann H.<br />
Structural insights into the redox-switch mechanism of the MarR/DUF24-type regulator HypR.<br />
Nucleic Acids Res. 2012, Jan 11. [Epub ahead of print]<br />
{{PubMed|22238377}}<br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=HypR&diff=148471
HypR
2012-01-16T19:49:15Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' MarR/DUF24-family transcription regulator, positively controls the nitroreductase gene ''[[hypO]]'' in response to disulfide stress <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
| ''hypR'' <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yybR''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || MarR/DUF24-family transcription regulator HypR <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || control of the nitroreductase gene ''[[hypO]]'' in response to disulfide stress (diamide, NaOCl)<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 14 kDa, 8.415 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 375 bp, 125 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cotF]]'', ''[[ppaC]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16091&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:yybR_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[transcription factors and their control]]}},<br />
{{SubtiWiki category|[[resistance against oxidative and electrophile stress]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[HypR regulon]]}}<br />
<br />
= The [[HypR regulon]]:=<br />
* ''[[hypR]]'', ''[[hypO]]'' <br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU40540<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yybR.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10013]<br />
<br />
=== Additional information===<br />
''hypR'' is autoregulated by disulfide stress<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' <br />
<br />
* '''Protein family:''' MarR/DUF24-family regulator<br />
<br />
* '''Paralogous protein(s):''' [[YdeP]],[[YkvN]]<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' Cys14 redox sensing Cys, has lower pKa of 6.36 {{PubMed|22238377}} <br />
<br />
* '''Domains:''' <br />
** 5 alpha helices, 2 beta sheets, MarR-fold with wHTH motif, alpha4 major groove recognition helix, beta2 and 3 form the wing; alpha5 dimer interface {{PubMed|22238377}} <br />
<br />
* '''Modification:''' <br />
** oxidized to Cys14-Cys49' intersubunit disulfides by disulfide stress {{PubMed|22238377}} <br />
** Cys14 and Cys49' are about 8-9 Angström apart in reduced HypR-Dimer, oxidation moves the major groove recognition alpha4 helices of the HypR dimer about 4 Angstroem towards each other that leads to activation of HypR {{PubMed|22238377}} <br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
<br />
* '''[[Localization]]:'''<br />
** cytoplasmic<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' <br />
** reduced HypRC14S dimer [http://www.pdb.org/pdb/explore.do?structureId=4A5N] {{PubMed|22238377}} <br />
** oxidized HypR C14-C49' intersubunit disulfide-linked dimer [http://www.pdb.org/pdb/explore.do?structureId=4A5M] {{PubMed|22238377}} <br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P37486 P37486]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40540]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''hypR'' (according to [http://dbtbs.hgc.jp/COG/prom/yybR.html DBTBS])<br />
<br />
* '''[[Sigma factor]]:''' <br />
<br />
* '''Regulation:''' <br />
** activated by disulfide stress conditions (diamide, NaOCl) ''in vivo'' and ''in vitro '' {{PubMed|22238377}} <br />
<br />
* '''Regulatory mechanism:'''<br />
** redox-controlled by Cys14-Cys49' intersubunit disulfide formation by diamide and NaOCl ''in vitro'' and ''in vivo'' {{PubMed|22238377}} <br />
<br />
* '''Additional information:''' <br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
* [[Haike Antelmann]],University of Greifswald, Germany<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
==Reviews==<br />
<br />
Antelmann H, Helmann JD.<br />
Thiol-based redox switches and gene regulation.<br />
Antioxid Redox Signal. 2011,14:1049-63.<br />
{{PubMed|20626317}}<br />
<br />
==Original articles==<br />
<br />
Palm GJ, Khanh Chi B, Waack P, Gronau K, Becher D, Albrecht D, Hinrichs W, Read RJ, Antelmann H.<br />
Structural insights into the redox-switch mechanism of the MarR/DUF24-type regulator HypR.<br />
Nucleic Acids Res. 2012, Jan 11. [Epub ahead of print]<br />
{{PubMed|22238377}}<br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=HypR&diff=148454
HypR
2012-01-15T11:20:06Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' MarR/DUF24-family transcription regulator, positively controls the nitroreductase gene ''[[yfkO]]'' (hypO) in response to disulfide stress <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
| ''yybR'' (hypR)<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''hypR''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || MarR/DUF24-family transcription regulator HypR <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || positively controls nitroreductase gene yfkO (hypO) in response to disulfide stress (diamide, NaOCl)<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 14 kDa, 8.415 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 375 bp, 125 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cotF]]'', ''[[ppaC]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16091&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:yybR_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[transcription factors and their control]]}},<br />
{{SubtiWiki category|[[resistance against oxidative and electrophile stress]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[YybR (HypR) regulon]]}}<br />
<br />
= The [[YybR (HypR) regulon]]:=<br />
* ''[[yybR]]'' (hypR), ''[[yfkO]]'' (hypO)<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU40540<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yybR.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10013]<br />
<br />
=== Additional information===<br />
hypR autoregulated by disulfide stress<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' <br />
<br />
* '''Protein family:''' MarR/DUF24-family regulator<br />
<br />
* '''Paralogous protein(s):''' YdeP,YkvN<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' Cys14 redox sensing Cys, has lower pKa of 6.36 {{PubMed|22238377}} <br />
<br />
* '''Domains:''' 5 alpha helices, 2 beta sheets, MarR-fold with wHTH motif, alpha4 major groove recognition helix, beta2 and 3 form the wing; alpha5 dimer interface {{PubMed|22238377}} <br />
* '''Modification:''' oxidized to Cys14-Cys49' intersubunit disulfides by disulfide stress {{PubMed|22238377}} <br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''Interactions:'''<br />
<br />
* '''Localization:''' cytoplasmic<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' <br />
reduced HypRC14S dimer [http://www.pdb.org/pdb/explore.do?structureId=4A5N]<br />
oxidized HypR C14-C49' intersubunit disulfide-linked dimer [http://www.pdb.org/pdb/explore.do?structureId=4A5M]<br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P37486 P37486]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40540]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''yybR'' (hypR)(according to [http://dbtbs.hgc.jp/COG/prom/yybR.html DBTBS])<br />
<br />
* '''[[Sigma factor]]:''' <br />
<br />
* '''Regulation:''' activated by disulfide stress conditions (diamide, NaOCl) in vivo and in vitro {{PubMed|22238377}} <br />
<br />
* '''Regulatory mechanism:''' redox-controlled by Cys14-Cys49' intersubunit disulfide formation by diamide and NaOCl in vitro and vivo {{PubMed|22238377}} <br />
<br />
* '''Additional information:''' Cys14 and Cys49' are about 8-9 Angstroem apart in reduced HypR-Dimer, oxidation moves the major groove recognition alpha4 helices of the HypR dimer about 4 Angstroem towards each other that leads to activation of HypR {{PubMed|22238377}} <br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
[[Haike Antelmann]],University of Greifswald, Germany<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
=Reviews=<br />
<pubmed>20626317</pubmed><br />
<br />
=Original articles=<br />
<pubmed>22238377</pubmed><br />
<br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=HypR&diff=148453
HypR
2012-01-15T11:16:56Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' MarR/DUF24-family transcription regulator, positively controls the nitroreductase gene ''[[yfkO]]'' (hypO) in response to disulfide stress <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
| ''yybR'' (hypR)<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''hypR''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || MarR/DUF24-family transcription regulator HypR <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || positively controls nitroreductase gene yfkO (hypO) in response to disulfide stress (diamide, NaOCl)<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 14 kDa, 8.415 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 375 bp, 125 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cotF]]'', ''[[ppaC]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16091&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:yybR_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[transcription factors and their control]]}},<br />
{{SubtiWiki category|[[resistance against oxidative and electrophile stress]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[YybR (HypR) regulon]]}}<br />
<br />
= The [[YybR (HypR) regulon]]:=<br />
* ''[[yybR]]'' (hypR), ''[[yfkO]]'' (hypO)<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU40540<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yybR.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10013]<br />
<br />
=== Additional information===<br />
hypR autoregulated by disulfide stress<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' <br />
<br />
* '''Protein family:''' MarR/DUF24-family regulator<br />
<br />
* '''Paralogous protein(s):''' YdeP,YkvN<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' Cys14 redox sensing Cys, has lower pKa of 6.36 {{PubMed|22238377}} <br />
<br />
* '''Domains:''' 5 alpha helices, 2 beta sheets, MarR-fold with wHTH motif, alpha4 major groove recognition helix, beta2 and 3 form the wing; alpha5 dimer interface {{PubMed|22238377}} <br />
* '''Modification:''' oxidized to Cys14-Cys49' intersubunit disulfides by disulfide stress {{PubMed|22238377}} <br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''Interactions:'''<br />
<br />
* '''Localization:''' cytoplasmic<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' <br />
reduced HypRC14S dimer [http://www.pdb.org/pdb/explore.do?structureId=4A5N]<br />
oxidized HypR C14-C49' intersubunit disulfide-linked dimer [http://www.pdb.org/pdb/explore.do?structureId=4A5M]<br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P37486 P37486]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40540]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''yybR'' (hypR)(according to [http://dbtbs.hgc.jp/COG/prom/yybR.html DBTBS])<br />
<br />
* '''[[Sigma factor]]:''' <br />
<br />
* '''Regulation:''' activated by disulfide stress conditions (diamide, NaOCl) in vivo and in vitro {{PubMed|22238377}} <br />
<br />
* '''Regulatory mechanism:''' redox-controlled by Cys14-Cys49' intersubunit disulfide formation by diamide and NaOCl in vitro and vivo {{PubMed|22238377}} <br />
<br />
* '''Additional information:''' Cys14 and Cys49' are about 8-9 Angstroem apart in reduced HypR-Dimer, oxidation moves the major groove recognition alpha4 helices of the HypR dimer about 4 Angstroem towards each other that leads to activation of HypR {{PubMed|22238377}} <br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
[[Haike Antelmann]],University of Greifswald, Germany<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
=Reviews=<br />
<pubmed>20626317 </pubmed><br />
<br />
=Original articles=<br />
<pubmed>22238377 </pubmed><br />
<br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=HypO&diff=148452
HypO
2012-01-13T09:17:03Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' NAD(P)H-flavin nitroreductase <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''yfkO'' (hypO)<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''hypO''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || NAD(P)H-flavin nitroreductase <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || probably involved in NaOCl and diamide detoxification<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 25 kDa, 5.667 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 663 bp, 221 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[treR]]'', ''[[yfkN]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12612&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:yfkO_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[electron transport/ other]]}},<br />
{{SubtiWiki category|[[resistance against oxidative and electrophile stress]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[HypR regulon]]}}<br />
<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU07830<br />
<br />
===Phenotypes of a mutant ===<br />
hypO ohrA mutant more sensitive to NaOCl stress than ohrA single mutant<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yfkO.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12931]<br />
<br />
=== Additional information===<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' <br />
<br />
* '''Protein family:''' nitroreductase family (according to Swiss-Prot)<br />
<br />
* '''Paralogous protein(s):'''<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:'''<br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''Interactions:'''<br />
<br />
* '''Localization:'''<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' <br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/O34475 O34475]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU07830]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''ykfO'' (hypO) (according to [http://dbtbs.hgc.jp/COG/prom/yfkO.html DBTBS])<br />
<br />
* '''[[Sigma factor]]:''' <br />
<br />
* '''Regulation:''' induced under disulfide stress conditions (diamide, NaOCl) ([[HypR]]) {{PubMed|22238377}} <br />
<br />
* '''Regulatory mechanism:''' <br />
** [[HypR]]:transcription activation {{PubMed|22238377}} <br />
<br />
* '''Additional information:'''<br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<pubmed>20727918,22238377</pubmed><br />
<br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=HypR&diff=148451
HypR
2012-01-13T09:13:06Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' MarR/DUF24-family transcription regulator, positively controls the nitroreductase gene ''[[yfkO]]'' (hypO) in response to disulfide stress <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
| ''yybR'' (hypR)<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''hypR''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || MarR/DUF24-family transcription regulator HypR <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || positively controls nitroreductase gene yfkO (hypO) in response to disulfide stress (diamide, NaOCl)<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 14 kDa, 8.415 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 375 bp, 125 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cotF]]'', ''[[ppaC]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16091&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:yybR_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[transcription factors and their control]]}},<br />
{{SubtiWiki category|[[resistance against oxidative and electrophile stress]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[YybR (HypR) regulon]]}}<br />
<br />
= The [[YybR (HypR) regulon]]:=<br />
* ''[[yybR]]'' (hypR), ''[[yfkO]]'' (hypO)<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU40540<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yybR.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10013]<br />
<br />
=== Additional information===<br />
hypR autoregulated by disulfide stress<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' <br />
<br />
* '''Protein family:''' MarR/DUF24-family regulator<br />
<br />
* '''Paralogous protein(s):''' YdeP,YkvN<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' Cys14 redox sensing Cys, has lower pKa of 6.36 {{PubMed|22238377}} <br />
<br />
* '''Domains:''' 5 alpha helices, 2 beta sheets, MarR-fold with wHTH motif, alpha4 major groove recognition helix, beta2 and 3 form the wing; alpha5 dimer interface {{PubMed|22238377}} <br />
* '''Modification:''' oxidized to Cys14-Cys49' intersubunit disulfides by disulfide stress {{PubMed|22238377}} <br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''Interactions:'''<br />
<br />
* '''Localization:''' cytoplasmic<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' <br />
reduced HypRC14S dimer [http://www.pdb.org/pdb/explore.do?structureId=4A5N]<br />
oxidized HypR C14-C49' intersubunit disulfide-linked dimer [http://www.pdb.org/pdb/explore.do?structureId=4A5M]<br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P37486 P37486]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40540]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''yybR'' (hypR)(according to [http://dbtbs.hgc.jp/COG/prom/yybR.html DBTBS])<br />
<br />
* '''[[Sigma factor]]:''' <br />
<br />
* '''Regulation:''' activated by disulfide stress conditions (diamide, NaOCl) in vivo and in vitro {{PubMed|22238377}} <br />
<br />
* '''Regulatory mechanism:''' redox-controlled by Cys14-Cys49' intersubunit disulfide formation by diamide and NaOCl in vitro and vivo {{PubMed|22238377}} <br />
<br />
* '''Additional information:''' Cys14 and Cys49' are about 8-9 Angstroem apart in reduced HypR-Dimer, oxidation moves the major groove recognition alpha4 helices of the HypR dimer about 4 Angstroem towards each other that leads to activation of HypR {{PubMed|22238377}} <br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
[[Haike Antelmann]],University of Greifswald, Germany<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
=Original articles=<br />
<br />
<pubmed>22238377</pubmed> <br />
<br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=HypR&diff=148450
HypR
2012-01-13T09:11:20Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' MarR/DUF24-family transcription regulator, positively controls the nitroreductase gene ''[[yfkO]]'' (hypO) in response to disulfide stress <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
| ''yybR'' (hypR)<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''hypR''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || MarR/DUF24-family transcription regulator HypR <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || positively controls nitroreductase gene yfkO (hypO) in response to disulfide stress (diamide, NaOCl)<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 14 kDa, 8.415 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 375 bp, 125 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cotF]]'', ''[[ppaC]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16091&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:yybR_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[transcription factors and their control]]}},<br />
{{SubtiWiki category|[[resistance against oxidative and electrophile stress]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[YybR (HypR) regulon]]}}<br />
<br />
= The [[YybR (HypR) regulon]]:=<br />
* ''[[yybR]]'' (hypR), ''[[yfkO]]'' (hypO)<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU40540<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yybR.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10013]<br />
<br />
=== Additional information===<br />
hypR autoregulated by disulfide stress<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' <br />
<br />
* '''Protein family:''' MarR/DUF24-family regulator<br />
<br />
* '''Paralogous protein(s):''' YdeP,YkvN<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' Cys14 redox sensing Cys, has lower pKa of 6.36 {{PubMed|22238377}} <br />
<br />
* '''Domains:''' 5 alpha helices, 2 beta sheets, MarR-fold with wHTH motif, alpha4 major groove recognition helix, beta2 and 3 form the wing; alpha5 dimer interface {{PubMed|22238377}} <br />
* '''Modification:''' oxidized to Cys14-Cys49' intersubunit disulfides by disulfide stress {{PubMed|22238377}} <br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''Interactions:'''<br />
<br />
* '''Localization:''' cytoplasmic<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' <br />
reduced HypRC14S dimer [http://www.pdb.org/pdb/explore.do?structureId=4A5N]<br />
oxidized HypR C14-C49' intersubunit disulfide-linked dimer [http://www.pdb.org/pdb/explore.do?structureId=4A5M]<br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P37486 P37486]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40540]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''yybR'' (hypR)(according to [http://dbtbs.hgc.jp/COG/prom/yybR.html DBTBS])<br />
<br />
* '''[[Sigma factor]]:''' <br />
<br />
* '''Regulation:''' activated by disulfide stress conditions (diamide, NaOCl) in vivo and in vitro {{PubMed|22238377}} <br />
<br />
* '''Regulatory mechanism:''' redox-controlled by Cys14-Cys49' intersubunit disulfide formation by diamide and NaOCl in vitro and vivo {{PubMed|22238377}} <br />
<br />
* '''Additional information:''' Cys14 and Cys49' are about 8-9 Angstroem apart in reduced HypR-Dimer, oxidation moves the major groove recognition alpha4 helices of the HypR dimer about 4 Angstroem towards each other that leads to activation of HypR {{PubMed|22238377}} <br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
[[Haike Antelmann]],University of Greifswald, Germany<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
=Original articles=<br />
<br />
<pubmed>22238377</pubmed> <br />
<br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=HypR&diff=148449
HypR
2012-01-13T09:07:00Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' MarR/DUF24-family transcription regulator, positively controls the nitroreductase gene ''[[yfkO]]'' (hypO) in response to disulfide stress <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
| ''yybR'' (hypR)<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''hypR''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || MarR/DUF24-family transcription regulator HypR <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || positively controls nitroreductase gene yfkO (hypO) in response to disulfide stress (diamide, NaOCl)<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 14 kDa, 8.415 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 375 bp, 125 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cotF]]'', ''[[ppaC]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16091&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:yybR_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[transcription factors and their control]]}},<br />
{{SubtiWiki category|[[resistance against oxidative and electrophile stress]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[YybR (HypR) regulon]]}}<br />
<br />
= The [[YybR (HypR) regulon]]:=<br />
* ''[[yybR]]'' (hypR), ''[[yfkO]]'' (hypO)<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU40540<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yybR.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10013]<br />
<br />
=== Additional information===<br />
hypR autoregulated by disulfide stress<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' <br />
<br />
* '''Protein family:''' MarR/DUF24-family regulator<br />
<br />
* '''Paralogous protein(s):''' YdeP,YkvN<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' Cys14 redox sensing Cys, has lower pKa of 6.36 {{PubMed|22238377}} <br />
<br />
* '''Domains:''' 5 alpha helices, 2 beta sheets, MarR-fold with wHTH motif, alpha4 major groove recognition helix, beta2 and 3 form the wing; alpha5 dimer interface {{PubMed|22238377}} <br />
* '''Modification:''' oxidized to Cys14-Cys49' intersubunit disulfides by disulfide stress {{PubMed|22238377}} <br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''Interactions:'''<br />
<br />
* '''Localization:''' cytoplasmic<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' <br />
reduced HypRC14S dimer [http://www.pdb.org/pdb/explore.do?structureId=4A5N]<br />
oxidized HypR C14-C49' intersubunit disulfide-linked dimer [http://www.pdb.org/pdb/explore.do?structureId=4A5M]<br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P37486 P37486]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40540]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''yybR'' (hypR)(according to [http://dbtbs.hgc.jp/COG/prom/yybR.html DBTBS])<br />
<br />
* '''[[Sigma factor]]:''' <br />
<br />
* '''Regulation:''' activated by disulfide stress conditions (diamide, NaOCl) in vivo and in vitro {{PubMed|22238377}} <br />
<br />
* '''Regulatory mechanism:''' redox-controlled by Cys14-Cys49' intersubunit disulfide formation by diamide and NaOCl in vitro and vivo {{PubMed|22238377}} <br />
<br />
<br />
* '''Additional information:''' Cys14 and Cys49' are about 8-9 Angstroem apart in reduced HypR-Dimer, oxidation moves the major groove recognition alpha4 helices of the HypR dimer about 4 Angstroem towards each other that leads to activation of HypR {{PubMed|22238377}} <br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
[[Haike Antelmann]],University of Greifswald, Germany<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
=Original articles=<br />
<br />
<pubmed>22238377</pubmed><br />
<br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=HypR&diff=148448
HypR
2012-01-13T08:58:48Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' MarR/DUF24-family transcription regulator, positively controls the nitroreductase gene ''[[yfkO]]'' (hypO) in response to disulfide stress <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
| ''yybR'' (hypR)<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''hypR''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || MarR/DUF24-family transcription regulator HypR <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || positively controls nitroreductase gene yfkO (hypO) in response to disulfide stress (diamide, NaOCl)<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 14 kDa, 8.415 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 375 bp, 125 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cotF]]'', ''[[ppaC]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16091&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:yybR_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[transcription factors and their control]]}},<br />
{{SubtiWiki category|[[resistance against oxidative and electrophile stress]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[YybR (HypR) regulon]]}}<br />
<br />
= The [[YybR (HypR) regulon]]:=<br />
* ''[[yybR]]'' (hypR), ''[[yfkO]]'' (hypO)<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU40540<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yybR.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10013]<br />
<br />
=== Additional information===<br />
hypR autoregulated by disulfide stress<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' <br />
<br />
* '''Protein family:''' MarR/DUF24-family regulator<br />
<br />
* '''Paralogous protein(s):''' YdeP,YkvN<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' Cys14 redox sensing Cys, has lower pKa of 6.36 {{PubMed|22238377}} <br />
<br />
* '''Domains:''' 5 alpha helices, 2 beta sheets, MarR-fold with wHTH motif, alpha4 major groove recognition helix, beta2 and 3 form the wing; alpha5 dimer interface {{PubMed|22238377}} <br />
* '''Modification:''' oxidized to Cys14-Cys49' intersubunit disulfides by disulfide stress {{PubMed|22238377}} <br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''Interactions:'''<br />
<br />
* '''Localization:''' cytoplasmic<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' tba <br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P37486 P37486]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40540]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''yybR'' (hypR)(according to [http://dbtbs.hgc.jp/COG/prom/yybR.html DBTBS])<br />
<br />
* '''[[Sigma factor]]:''' <br />
<br />
* '''Regulation:''' activated by disulfide stress conditions (diamide, NaOCl) in vivo and in vitro {{PubMed|22238377}} <br />
<br />
* '''Regulatory mechanism:''' redox-controlled by Cys14-Cys49' intersubunit disulfide formation by diamide and NaOCl in vitro and vivo {{PubMed|22238377}} <br />
<br />
<br />
* '''Additional information:''' Cys14 and Cys49' are about 8-9 Angstroem apart in reduced HypR-Dimer, oxidation moves the major groove recognition alpha4 helices of the HypR dimer about 4 Angstroem towards each other that leads to activation of HypR {{PubMed|22238377}} <br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
[[Haike Antelmann]],University of Greifswald, Germany<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
=Original articles=<br />
<br />
<pubmed>22238377</pubmed><br />
<br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=HypR&diff=148447
HypR
2012-01-13T08:56:19Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' MarR/DUF24-family transcription regulator, positively controls the nitroreductase gene ''[[yfkO]]'' (hypO) in response to disulfide stress <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
| ''yybR'' (hypR)<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''hypR''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || MarR/DUF24-family transcription regulator HypR <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || positively controls nitroreductase gene yfkO (hypO) in response to disulfide stress (diamide, NaOCl)<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 14 kDa, 8.415 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 375 bp, 125 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cotF]]'', ''[[ppaC]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16091&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:yybR_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[transcription factors and their control]]}},<br />
{{SubtiWiki category|[[resistance against oxidative and electrophile stress]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[YybR (HypR) regulon]]}}<br />
<br />
= The [[YybR (HypR) regulon]]:=<br />
* ''[[yybR]]'' (hypR), ''[[yfkO]]'' (hypO)<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU40540<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yybR.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10013]<br />
<br />
=== Additional information===<br />
hypR autoregulated by disulfide stress<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' <br />
<br />
* '''Protein family:''' MarR/DUF24-family regulator<br />
<br />
* '''Paralogous protein(s):''' YdeP,YkvN<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' Cys14 redox sensing Cys, has lower pKa of 6.36 {{PubMed|22238377}} <br />
<br />
* '''Domains:''' 5 alpha helices, 2 beta sheets, MarR-fold with wHTH motif, alpha4 major groove recognition helix, beta2 and 3 form the wing; alpha5 dimer interface {{PubMed|22238377}} <br />
* '''Modification:''' oxidized to Cys14-Cys49' intersubunit disulfides by disulfide stress {{PubMed|22238377}} <br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''Interactions:'''<br />
<br />
* '''Localization:''' cytoplasmic<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' tba <br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P37486 P37486]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40540]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''yybR'' (hypR)(according to [http://dbtbs.hgc.jp/COG/prom/yybR.html DBTBS])<br />
<br />
* '''[[Sigma factor]]:''' <br />
<br />
* '''Regulation:''' activated by disulfide stress conditions (diamide, NaOCl) in vivo and in vitro {{PubMed|22238377}} <br />
<br />
* '''Regulatory mechanism:''' redox-controlled by Cys14-Cys49' intersubunit disulfide formation by diamide and NaOCl in vitro and vivo {{PubMed|22238377}} <br />
<br />
<br />
* '''Additional information:''' Cys14 and Cys49' are about 8-9 Angstroem apart in reduced HypR-Dimer, oxidation moves the major groove recognition alpha4 helices of the HypR dimer about 4 Angstroem towards each other that leads to activation of HypR {{PubMed|22238377}} <br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
[[Haike Antelmann]],University of Greifswald, Germany<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<pubmed>22238377</pubmed><br />
<br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=HypR&diff=148443
HypR
2012-01-13T08:52:13Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' MarR/DUF24-family transcription regulator, positively controls the nitroreductase gene ''[[yfkO]]'' (hypO) in response to disulfide stress <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
| ''yybR'' (hypR)<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''hypR''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || MarR/DUF24-family transcription regulator HypR <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || positively controls nitroreductase gene yfkO (hypO) in response to disulfide stress (diamide, NaOCl)<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 14 kDa, 8.415 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 375 bp, 125 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cotF]]'', ''[[ppaC]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16091&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:yybR_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[transcription factors and their control]]}},<br />
{{SubtiWiki category|[[resistance against oxidative and electrophile stress]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[YybR (HypR) regulon]]}}<br />
<br />
= The [[YybR (HypR) regulon]]:=<br />
* ''[[yybR]]'' (hypR), ''[[yfkO]]'' (hypO)<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU40540<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yybR.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10013]<br />
<br />
=== Additional information===<br />
hypR autoregulated by disulfide stress<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' <br />
<br />
* '''Protein family:''' MarR/DUF24-family regulator<br />
<br />
* '''Paralogous protein(s):''' YdeP,YkvN<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' Cys14 redox sensing Cys, has lower pKa of 6.36 {{PubMed|22238377}} <br />
<br />
* '''Domains:''' 5 alpha helices, 2 beta sheets, MarR-fold with wHTH motif, alpha4 major groove recognition helix, beta2 and 3 form the wing; alpha5 dimer interface {{PubMed|22238377}} <br />
* '''Modification:''' oxidized to Cys14-Cys49' intersubunit disulfides by disulfide stress {{PubMed|22238377}} <br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''Interactions:'''<br />
<br />
* '''Localization:''' cytoplasmic<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' tba <br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P37486 P37486]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40540]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''yybR'' (hypR)(according to [http://dbtbs.hgc.jp/COG/prom/yybR.html DBTBS])<br />
<br />
* '''[[Sigma factor]]:''' <br />
<br />
* '''Regulation:''' activated by disulfide stress conditions (diamide, NaOCl) in vivo and in vitro {{PubMed|22238377}} <br />
<br />
* '''Regulatory mechanism:''' redox-controlled by Cys14-Cys49' intersubunit disulfide formation by diamide and NaOCl in vitro and vivo {{PubMed|22238377}} <br />
<br />
<br />
* '''Additional information:''' Cys14 and Cys49' are about 8-9 Angstroem apart in reduced HypR-Dimer, oxidation moves the major groove recognition alpha4 helices of the HypR dimer about 4 Angstroem towards each other that leads to activation of HypR {{PubMed|22238377}} <br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
[[Haike Antelmann]],University of Greifswald, Germany<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<pubmed>22238377</pubmed><br />
<br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=HypR&diff=148442
HypR
2012-01-13T08:47:57Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' MarR/DUF24-family transcription regulator, positively controls the nitroreductase gene ''[[yfkO]]'' (hypO) in response to disulfide stress <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
| ''yybR'' (hypR)<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''hypR''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || MarR/DUF24-family transcription regulator HypR <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || positively controls nitroreductase gene yfkO (hypO) in response to disulfide stress (diamide, NaOCl)<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 14 kDa, 8.415 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 375 bp, 125 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cotF]]'', ''[[ppaC]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16091&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:yybR_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[transcription factors and their control]]}},<br />
{{SubtiWiki category|[[resistance against oxidative and electrophile stress]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[YybR (HypR) regulon]]}}<br />
<br />
= The [[YybR (HypR) regulon]]:=<br />
* ''[[yybR]]'' (hypR), ''[[yfkO]]'' (hypO)<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU40540<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yybR.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10013]<br />
<br />
=== Additional information===<br />
hypR autoregulated by disulfide stress<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' <br />
<br />
* '''Protein family:''' MarR/DUF24-family regulator<br />
<br />
* '''Paralogous protein(s):''' YdeP,YkvN<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' Cys14 redox sensing Cys, has lower pKa of 6.36 <br />
<br />
* '''Domains:''' 5 alpha helices, 2 beta sheets, MarR-fold with wHTH motif, alpha4 major groove recognition helix, beta2 and 3 form the wing; alpha5 dimer interface<br />
<br />
* '''Modification:''' oxidized to Cys14-Cys49' intersubunit disulfides by disulfide stress<br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''Interactions:'''<br />
<br />
* '''Localization:''' cytoplasmic<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' tba <br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P37486 P37486]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40540]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''yybR'' (hypR)(according to [http://dbtbs.hgc.jp/COG/prom/yybR.html DBTBS])<br />
<br />
* '''[[Sigma factor]]:''' <br />
<br />
* '''Regulation:''' activated by disulfide stress conditions (diamide, NaOCl) in vivo and in vitro<br />
<br />
* '''Regulatory mechanism:''' redox-controlled by Cys14-Cys49' intersubunit disulfide formation by diamide and NaOCl in vitro and vivo<br />
<br />
* '''Additional information:''' Cys14 and Cys49' are about 8-9 Angstroem apart in reduced HypR-Dimer, oxidation moves the major groove recognition alpha4 helices of the HypR dimer about 4 Angstroem towards each other that leads to activation of HypR <br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
[[Haike Antelmann]],University of Greifswald, Germany<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<pubmed>22238377</pubmed><br />
<br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=HypR&diff=148441
HypR
2012-01-13T08:46:02Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' MarR/DUF24-family transcription regulator, positively controls the nitroreductase gene ''[[yfkO]]'' (hypO) in response to disulfide stress <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
| ''yybR'' (hypR)<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''hypR''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || MarR/DUF24-family transcription regulator HypR <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || positively controls nitroreductase gene yfkO (hypO) in response to disulfide stress (diamide, NaOCl)<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 14 kDa, 8.415 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 375 bp, 125 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cotF]]'', ''[[ppaC]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16091&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:yybR_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[transcription factors and their control]]}},<br />
{{SubtiWiki category|[[resistance against oxidative and electrophile stress]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[YybR (HypR) regulon]]}}<br />
<br />
= The [[YybR (HypR) regulon]]:=<br />
* ''[[yybR]]'' (hypR), ''[[yfkO]]'' (hypO)<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU40540<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yybR.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10013]<br />
<br />
=== Additional information===<br />
hypR autoregulated by disulfide stress<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' <br />
<br />
* '''Protein family:''' MarR/DUF24-family regulator<br />
<br />
* '''Paralogous protein(s):''' YdeP,YkvN<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' Cys14 redox sensing Cys, has lower pKa of 6.36 <br />
<br />
* '''Domains:''' 5 alpha helices, 2 beta sheets, MarR-fold with wHTH motif, alpha4 major groove recognition helix, beta2 and 3 form the wing; alpha5 dimer interface<br />
<br />
* '''Modification:''' oxidized to Cys14-Cys49' intersubunit disulfides by disulfide stress<br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''Interactions:'''<br />
<br />
* '''Localization:''' cytoplasmic<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' tba <br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P37486 P37486]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU40540]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' ''yybR'' (hypR)(according to [http://dbtbs.hgc.jp/COG/prom/yybR.html DBTBS])<br />
<br />
* '''[[Sigma factor]]:''' <br />
<br />
* '''Regulation:''' activated by disulfide stress conditions (diamide, NaOCl) in vivo and in vitro<br />
<br />
* '''Regulatory mechanism:''' redox-controlled by Cys14-Cys49' intersubunit disulfide formation by diamide and NaOCl in vitro and vivo<br />
<br />
* '''Additional information:''' Cys14 and Cys49' are about 8-9 Angstroem apart in reduced HypR-Dimer, oxidation moves the major groove recognition alpha4 helices of the HypR dimer about 4 Angstroem towards each other that leads to activation of HypR <br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
[[Haike Antelmann]],University of Greifswald, Germany<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
<pubmed>22238377</pubmed><br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=YodB&diff=148033
YodB
2011-12-26T11:20:54Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' MarR/DUF24-family transcription repressor of ''[[azoR1]]'', ''[[catD]]-[[catE]]'' and ''[[yodC]]'' expression <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''yodB''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || MarR/DUF24-family transcription repressor <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of quinone and diamide detoxification<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 12 kDa, 4.737 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 336 bp, 112 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yodA]]'', ''[[yodC]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13845&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:yodB_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[transcription factors and their control]]}},<br />
{{SubtiWiki category|[[resistance against oxidative and electrophile stress]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[YodB regulon]]}}<br />
<br />
=The [[YodB regulon]]:=<br />
* ''[[azoR1]]'', ''[[catD]]-[[catE]]'', ''[[yodB]]'', ''[[yodC]]''<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU19540<br />
<br />
===Phenotypes of a mutant ===<br />
increased resistance to catechol, quinones and diamide {{PubMed|20639328}} <br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' no entry<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13531]<br />
<br />
=== Additional information===<br />
<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' <br />
<br />
* '''Protein family:''' MarR/DUF24-family <br />
<br />
* '''Paralogous protein(s):''' [[CatR]]<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:''' redox-controlled by intersubunit disulfide formation of Cys6 and Cys101' in response to quinones and diamide<br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''[[SubtInteract|Interactions]]:''' <br />
<br />
* '''[[Localization]]:'''<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' <br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/O34844 O34844]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU19540]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' <br />
<br />
* '''[[Sigma factor]]:''' <br />
<br />
* '''Regulation:''' <br />
** subject to autorepression {{PubMed|21749987}} <br />
<br />
* '''Regulatory mechanism:''' <br />
** YodB: transcription repression {{PubMed|21749987}} <br />
<br />
* '''Additional information:''' <br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
[[Haike Antelmann]],University of Greifswald, Germany<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
==Reviews==<br />
<pubmed>20626317</pubmed><br />
<br />
==Original Publications==<br />
<pubmed>17158660,17407181,18208493,20639328,20652907,21749987</pubmed><br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=YodB&diff=148032
YodB
2011-12-26T11:19:07Z
<p>Antelmann: </p>
<hr />
<div>* '''Description:''' MarR/DUF24-family transcription repressor of ''[[azoR1]]'', ''[[catD]]-[[catE]]'' and ''[[yodC]]'' expression <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''yodB''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || MarR/DUF24-family transcription repressor <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of quinone and diamide detoxification<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 12 kDa, 4.737 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 336 bp, 112 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yodA]]'', ''[[yodC]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13845&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:yodB_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[transcription factors and their control]]}},<br />
{{SubtiWiki category|[[resistance against oxidative and electrophile stress]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[YodB regulon]]}}<br />
<br />
=The [[YodB regulon]]:=<br />
* ''[[azoR1]]'', ''[[catD]]-[[catE]]'', ''[[yodB]]'', ''[[yodC]]''<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU19540<br />
<br />
===Phenotypes of a mutant ===<br />
increased resistance to catechol, quinones and diamide {{PubMed|20639328}} <br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' no entry<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13531]<br />
<br />
=== Additional information===<br />
<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' <br />
<br />
* '''Protein family:''' MarR/DUF24-family <br />
<br />
* '''Paralogous protein(s):''' [[CatR]]<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:''' redox-controlled by intersubunit disulfide formation of Cys6 and Cys101' in response to quinones and diamide<br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''[[SubtInteract|Interactions]]:''' <br />
<br />
* '''[[Localization]]:'''<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' <br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/O34844 O34844]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU19540]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' <br />
<br />
* '''[[Sigma factor]]:''' <br />
<br />
* '''Regulation:''' <br />
** subject to autorepression {{PubMed|21749987}} <br />
<br />
* '''Regulatory mechanism:''' <br />
** YodB: transcription repression {{PubMed|21749987}} <br />
<br />
* '''Additional information:''' <br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
[[Haike Antelmann]],University of Greifswald, Germany<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<br />
==Reviews==<br />
<pubmed>20626317</pubmed><br />
<br />
==Original Publications==<br />
<pubmed>20626317,17158660,17407181,18208493,20639328,20652907,21749987</pubmed><br />
<br />
[[Category:Protein-coding genes]]</div>
Antelmann