SubtiWiki - User contributions [en]

GapA

2009-06-11T11:10:33Z

Cadu Cunha: /* Extended information on the protein */

* '''Description:''' Glyceraldehyde 3-phosphate dehydrogenase, NAD-dependent, glycolytic enzyme <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''gapA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || Yes [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 (PubMed)]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || glyceraldehyde 3-phosphate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || catabolic enzyme in glycolysis
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 35.7 kDa, 5.03
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1005 bp, 335 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cggR]]'', ''[[pgk]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15399]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:gapA_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33940

===Phenotypes of a mutant ===

* Essential [http://www.ncbi.nlm.nih.gov/pubmed/17114254 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]

* '''SubtiList entry:'''[http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10827]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' D-glyceraldehyde 3-phosphate + phosphate + NAD<sup>+</sup> = 3-phospho-D-glyceroyl phosphate + NADH (according to Swiss-Prot)
** This reaction is part of the glycolysis.

* '''Protein family:''' glyceraldehyde-3-phosphate dehydrogenase family (according to Swiss-Prot)

* '''Paralogous protein(s):''' [[GapB]]

=== Extended information on the protein ===

* '''Kinetic information:''' Michaelis-Menten [http://www.ncbi.nlm.nih.gov/sites/entrez/10799476 PubMed]

* '''Domains:'''

* '''Modification:'''
** 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]
** Reversible thiol modifications after exposure to toxic quinones [http://www.ncbi.nlm.nih.gov/sites/entrez/18673455 PubMed]

* '''Cofactor(s):''' NAD+ (do not accept NADP+) [http://www.ncbi.nlm.nih.gov/sites/entrez/10799476 PubMed]

* '''Effectors of protein activity:'''

* '''Interactions:'''
** 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]
** 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]

* '''Localization:''' cytoplasm (according to Swiss-Prot), Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/14600241 PubMed], loosely membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:'''
** [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3CMC 3CMC] (from ''Geobacillus stearothermophilus'')
** [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)

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P09124 P09124]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33940]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.2.1.12 1.2.1.12]

=== Additional information===

GAP dehydrogenases from different sources (incl. ''Geobacillus stearothermophilus'') were shown to cleave RNA ([http://www.ncbi.nlm.nih.gov/sites/entrez/12359717 PubMed]). 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]).

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpi]]-[[pgm]]-[[eno]]''
** ''[[cggR]]-[[gapA]]''

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. The processing event requires the [[Rny]] protein.

* '''Sigma factor:''' [[SigA]]

* '''Regulation:''' expression activated by glucose (10 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed], [[CggR]] represses the operon in the absence of glycolytic sugars [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12622823 PubMed]

* '''Regulatory mechanism:''' repression

* '''Database entries:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html DBTBS]

* '''Additional information:''' 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]).

=Biological materials =

* '''Mutant:''' essential

* '''Expression vector:'''
** pGP90 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
** pGP704 (N-terminal His-tag, in [[pWH844]]) (available in [[Stülke]] lab)

* '''lacZ fusion:''' pGP506 (in [[pAC7]]), pGP512 (in [[pAC6]]) (available in [[Stülke]] lab)

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:''' available in [[Stülke]] lab

=Labs working on this gene/protein=

[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France

[[Stülke|Jörg Stülke]], University of Göttingen, Germany
[http://wwwuser.gwdg.de/~genmibio/stuelke.html homepage]

=Your additional remarks=

=References=

<pubmed> 12850135,19193632, 18673455 , 17726680,16479537,12622823,12359717,10799476,17505547,11489127,12123463,17218307,12634343,17142398,17114254,10559165 </pubmed>

GapA

2009-06-11T11:09:51Z

Cadu Cunha: /* Basic information/ Evolution */

* '''Description:''' Glyceraldehyde 3-phosphate dehydrogenase, NAD-dependent, glycolytic enzyme <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''gapA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || Yes [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 (PubMed)]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || glyceraldehyde 3-phosphate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || catabolic enzyme in glycolysis
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 35.7 kDa, 5.03
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1005 bp, 335 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cggR]]'', ''[[pgk]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15399]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:gapA_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33940

===Phenotypes of a mutant ===

* Essential [http://www.ncbi.nlm.nih.gov/pubmed/17114254 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]

* '''SubtiList entry:'''[http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10827]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' D-glyceraldehyde 3-phosphate + phosphate + NAD<sup>+</sup> = 3-phospho-D-glyceroyl phosphate + NADH (according to Swiss-Prot)
** This reaction is part of the glycolysis.

* '''Protein family:''' glyceraldehyde-3-phosphate dehydrogenase family (according to Swiss-Prot)

* '''Paralogous protein(s):''' [[GapB]]

=== Extended information on the protein ===

* '''Kinetic information:''' Michaelis-Menten [http://www.ncbi.nlm.nih.gov/sites/entrez/10799476 PubMed]

* '''Domains:'''

* '''Modification:'''
** 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]
** Reversible thiol modifications after exposure to toxic quinones [http://www.ncbi.nlm.nih.gov/sites/entrez/18673455 PubMed]

* '''Cofactor(s):''' NAD+ (do not accept NADP+) http://www.ncbi.nlm.nih.gov/sites/entrez/10799476 PubMed

* '''Effectors of protein activity:'''

* '''Interactions:'''
** 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]
** 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]

* '''Localization:''' cytoplasm (according to Swiss-Prot), Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/14600241 PubMed], loosely membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:'''
** [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3CMC 3CMC] (from ''Geobacillus stearothermophilus'')
** [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)

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P09124 P09124]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33940]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.2.1.12 1.2.1.12]

=== Additional information===

GAP dehydrogenases from different sources (incl. ''Geobacillus stearothermophilus'') were shown to cleave RNA ([http://www.ncbi.nlm.nih.gov/sites/entrez/12359717 PubMed]). 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]).

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpi]]-[[pgm]]-[[eno]]''
** ''[[cggR]]-[[gapA]]''

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. The processing event requires the [[Rny]] protein.

* '''Sigma factor:''' [[SigA]]

* '''Regulation:''' expression activated by glucose (10 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed], [[CggR]] represses the operon in the absence of glycolytic sugars [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12622823 PubMed]

* '''Regulatory mechanism:''' repression

* '''Database entries:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html DBTBS]

* '''Additional information:''' 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]).

=Biological materials =

* '''Mutant:''' essential

* '''Expression vector:'''
** pGP90 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
** pGP704 (N-terminal His-tag, in [[pWH844]]) (available in [[Stülke]] lab)

* '''lacZ fusion:''' pGP506 (in [[pAC7]]), pGP512 (in [[pAC6]]) (available in [[Stülke]] lab)

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:''' available in [[Stülke]] lab

=Labs working on this gene/protein=

[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France

[[Stülke|Jörg Stülke]], University of Göttingen, Germany
[http://wwwuser.gwdg.de/~genmibio/stuelke.html homepage]

=Your additional remarks=

=References=

<pubmed> 12850135,19193632, 18673455 , 17726680,16479537,12622823,12359717,10799476,17505547,11489127,12123463,17218307,12634343,17142398,17114254,10559165 </pubmed>

FbaA

2009-06-11T11:08:14Z

Cadu Cunha: /* Database entries */

* '''Description:''' fructose 1,6-bisphosphate aldolase, glycolytic/ gluconeogenic enzyme<br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''fbaA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''fba, fba1, tsr ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || fructose-1,6-bisphosphate aldolase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30,2 kDa, 5.03
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 855 bp, 285 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[spo0F]]'', ''[[ywjH]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15729]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:fbaA_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU37120

===Phenotypes of a mutant ===

*Essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/fbaA-ywjH.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10412]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate (according to Swiss-Prot)

* '''Protein family:''' class II fructose-bisphosphate aldolase family (according to Swiss-Prot)
* '''Paralogous protein(s):''' [[FbaB]]

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/sites/entrez/15125960 PubMed]

* '''Domains:'''
** 2 x Dihydroxyacetone phosphate binding domain (210–212), (231–234)

* '''Modification:''' phosphorylation on Thr-212 and Thr-234 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):''' Zn2+ (Metalloenzyme)

* '''Effectors of protein activity:'''
** Inhibited by alpha-ketoglutarate, oxaloacetate and pyruvate [http://www.ncbi.nlm.nih.gov/pubmed/24624 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/15125960 PubMed]
** Activated by NH4+ [http://www.ncbi.nlm.nih.gov/sites/entrez/15125960 PubMed]

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P13243 P13243]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU37120]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.1.2.13 4.1.2.13]

=== Additional information===

Binds 2 zinc ions per subunit. One is catalytic and the other provides a structural contribution

=Expression and regulation=

* '''Operon:'''
**''fbaA'' [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]
**''fbaA-[[ywjH]]'' [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Sigma factor:'''

* '''Regulation:''' constitutively expressed [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:''' pGP395 (N-terminal His-tag, in [[pWH844]]), pGP88 (N-terminal Strep-tag, for [[SPINE]], expression in ''B. subtilis'', in [[pGP380]])

* '''lacZ fusion:''' pGP601 (in [[pAC6]])

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>17218307, 15125960, 24624 </pubmed>
# Trach K, Chapman JW & Piggot P (1988) Complete sequence and transcriptional analysis of the ''spo0F'' region of the ''Bacillus subtilis'' chromosome ''J Bacteriol.'' '''170:''' 4194-4208. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+2457578 PubMed]
# Ludwig H, Homuth G & Schmalisch M (2001) Transcription of glycolytic genes and operons in ''Bacillus subtilis'': evidence for the presence of multiple levels of control of the ''gapA'' operon ''Mol Microbiol.'' '''41:''' 409-422. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]

Tpi

2009-06-11T11:06:43Z

Cadu Cunha: /* References */

* '''Description:''' triose phosphate isomerase, glycolytic/ gluconeogenic enzyme<br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''tpi''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''tpiA''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || triosephosphate isomerase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26,9 kDa, 4.79
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 759 bp, 253 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pgk]]'', ''[[pgm]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15397]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:tpi_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33920

===Phenotypes of a mutant ===

* Essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10897]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' D-glyceraldehyde 3-phosphate = dihydroxyacetone phosphate (according to Swiss-Prot)

* '''Protein family:''' triosephosphate isomerase family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-213 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:''' inhibited by 2-phosphoglycolate (in ''B. stearothermophilus'') [http://www.ncbi.nlm.nih.gov/sites/entrez/8580851 PubMed]

* '''Interactions:'''

* '''Localization:''' cytoplasm (according to Swiss-Prot), cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1BTM 1BTM] (complex with 2-phosphoglycolic acid, Geobacillus stearothermophilus), complex with 2-phosphpoglycolic acid, ''Geobacillus stearothermophilus'' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=48255 NCBI]

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P27876 P27876]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33920]

* '''E.C. number:''' [http://www.expasy.org/enzyme/5.3.1.1 5.3.1.1] 5.3.1.1]

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]''
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]''

* '''Sigma factor:''' [[SigA]]

* '''Regulation:''' expression activated by glucose (2.8 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
**''[[cggR]]'': neg. regulated by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed], induced by sugar
**''[[pgk]]'': constitutive [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Regulatory mechanism:''' transcription repression by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:''' pGP394 (N-terminal His-tag, in [[pWH844]]), pGP89 (N-terminal Strep-tag, for [[SPINE]], expression in B. subtilis), available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>12850135 11489127 17505547 8021172 17218307 8580851 </pubmed>
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
# Ludwig, H., Homuth, G., Schmalisch, M., Dyka, F. M., Hecker, M., and Stülke, J. (2001) Transcription of glycolytic genes and operons in ''Bacillus subtilis'': evidence for the presence of multiple levels of control of the ''gapA'' operon. Mol Microbiol 41, 409-422.[http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]
# Jannière, L., Canceill, D., Suski, C., Kanga, S., Dalmais, B., Lestini, R., Monnier, A. F., Chapuis, J., Bolotin, A., Titok, M., Le Chatelier, E., and Ehrlich, S. D. (2007) Genetic evidence for a link between glycolysis and DNA replication. PLoS ONE 2, e447. [http://www.ncbi.nlm.nih.gov/sites/entrez/17505547 PubMed]
# Leyva-Vazquez, M. A., and Setlow, P. (1994) Cloning and nucleotide sequences of the genes encoding triose phosphate isomerase, phosphoglycerate mutase, and enolase from Bacillus subtilis. J Bacteriol 176: 3903-3910. [http://www.ncbi.nlm.nih.gov/sites/entrez/8021172 PubMed]
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]

Pgk

2009-06-11T11:05:02Z

Cadu Cunha: /* References */

* '''Description:''' phosphoglycerate kinase, glycolytic/ gluconeogenic enzyme<br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pgk''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphoglycerate kinase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 42,0 kDa, 4.77
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1182 bp, 394 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gapA]]'', ''[[tpi]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15398]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:pgk_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33930

===Phenotypes of a mutant ===

* Essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11062]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + 3-phospho-D-glycerate = ADP + 1,3-bisphosphoglycerate (according to Swiss-Prot)

* '''Protein family:''' phosphoglycerate kinase family (according to Swiss-Prot)
* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Two Substrate Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/7154941 PubMed]

* '''Domains:'''
** nucleotide binding domain (ATP) (350–353)
** 2x substrate binding domain (21–23), (59–62)

* '''Modification:''' phosphorylation on Ser-183 AND Thr-299 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]

* '''Cofactor(s):''' Mg2+ or Mn2+ [http://www.ncbi.nlm.nih.gov/pubmed/7154941 PubMed]

* '''Effectors of protein activity:'''
** Inhibited by Co2+, NDP and NMP [http://www.ncbi.nlm.nih.gov/pubmed/7154941 PubMed]

* '''Interactions:'''

* '''Localization:''' cytoplasm (according to Swiss-Prot), Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1PHP 1PHP] (Geobacillus stearothermophilus), ''Geobacillus stearothermophilus'' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=57113 NCBI]

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P40924 P40924]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33930]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.2.3 2.7.2.3]

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]''
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]''

* '''Sigma factor:''' [[SigA]]

* '''Regulation:''' expression activated by glucose (2.8 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
**''[[cggR]]'': induced by sugar [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]
**''[[pgk]]'': constitutive [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Regulatory mechanism:''' transcription repression by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:''' pGP1102 (N-terminal His-tag, in [[pWH844]]), pGP95 (N-terminal Strep-tag, in [[pGP172]]), pGP91 (N-terminal Strep-tag, for [[SPINE]], expression in ''B. subtilis'', in [[pGP380]]), available in [[Stülke]] lab

* '''lacZ fusion:''' pGP514 (in [[pAC6]]), a series of promoter deletion variants is also available in [[pAC6]], available in [[Stülke]] lab

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed> 16479537, 12850135 , 17726680, 11489127 ,17505547 , 17218307 7154941 </pubmed>

Pgm

2009-06-11T11:02:30Z

Cadu Cunha: /* References */

* '''Description:''' phosphoglycerate mutase, glycolytic / gluconeogenic enzyme<br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pgm''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''gpmI''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || 2,3-bisphosphoglycerate-independent <br/>phosphoglycerate mutase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis / gluconeogenesis
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56,1 kDa, 5.21
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1533 bp, 511 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[tpi]]'', ''[[eno]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15396]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:pgm_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU33910

===Phenotypes of a mutant ===

* Essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10898]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 2-phospho-D-glycerate = 3-phospho-D-glycerate (according to Swiss-Prot)

* '''Protein family:''' BPG-independent phosphoglycerate mutase family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/33963 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-62 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]

* '''Cofactor(s):''' Mn2+

* '''Effectors of protein activity:'''
** Inhibited by diverse divalent heavy-metal ions, EDTA and 2,3-butanedione [http://www.ncbi.nlm.nih.gov/sites/entrez/33963 PubMed]
** 2,3-Diphosphoglycerate has NO role on this enzyme regulation [http://www.ncbi.nlm.nih.gov/sites/entrez/33963 PubMed]

* '''Interactions:''' Pgm-[[PfkA]]

* '''Localization:''' Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1EJJ 1EJJ] (Geobacillus stearothermophilus, complex with 3-phosphoglycerate), [http://www.rcsb.org/pdb/explore.do?structureId=1EQJ 1EQJ] (Geobacillus stearothermophilus, complex with 2-phosphoglycerate), ''Geobacillus stearothermophilus'', complex with 2-phosphoglycerate [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=16359 NCBI], ''Geobacillus stearothermophilus'', complex with 3-phosphoglycerate [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=15578 NCBI]

* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P39773]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33910]

* '''E.C. number:''' [http://www.expasy.org/enzyme/5.4.2.1 5.4.2.1]]

=== Additional information===

=Expression and regulation=

* '''Operon:'''
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]''
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]''

* '''Sigma factor:''' [[SigA]]

* '''Regulation:''' expression activated by glucose (7.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
''[[cggR]]'': neg. regulated by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed], induced by sugar

''[[pgk]]'': constitutive [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Regulatory mechanism:''' transcription repression by [[CggR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11489127 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:''' pGP1101 (N-terminal His-tag, in [[pWH844]]), pGP396 (Pgm-S62A, N-terminal His-tag, in [[pWH844]]), pGP92 (N-terminal Strep-tag, for [[SPINE]], expression in B. subtilis, in [[pGP380]]), available in [[Stülke]] lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

[[Stülke|Jörg Stülke]], University of Göttingen, Germany [http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]

[[Jedrzejas|Mark J. Jedrzejas]], Research Center Oakland, CA, USA [http://www.chori.org/Principal_Investigators/Jedrzejas_Mark_J/jedrzejas_research.html Homepage]

=Your additional remarks=

=References=

<pubmed>16479537, 12850135,17726680,17505547, 8021172,11489127, 10388626,10747010, 10764795, 11712498, 12729763, 17085493, 17218307 33963 </pubmed>

PfkA

2009-06-11T11:01:09Z

Cadu Cunha: /* References */

* '''Description:''' phosphofructokinase, glycolytic enzyme <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pfkA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''pfk''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || 6-phosphofructokinase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || catabolic enzyme in glycolysis
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 34,1 kDa, 6.14
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 957 bp, 319 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[accA]]'', ''[[pyk]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14879]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:pfkA_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29190

===Phenotypes of a mutant ===

*Essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pfkA-pyk-ytzA.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12644]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + D-fructose 6-phosphate = ADP + D-fructose 1,6-bisphosphate (according to Swiss-Prot)

* '''Protein family:''' phosphofructokinase family (according to Swiss-Prot) phosphofructokinase family

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Allosteric Regulation (Reversible) [http://www.ncbi.nlm.nih.gov/pubmed/4269800 PubMed]

* '''Domains:'''
** 3 x nucleotide binding domain (ATP) (21–25), (154–158), (171–187)

* '''Modification:'''

* '''Cofactor(s):''' Mg2+

* '''Effectors of protein activity:'''
** Inhibited by citrate, PEP (Hill Coefficient 3) and Ca2+ (competes with Mg2+) in ''B. licheniformes'' [http://www.ncbi.nlm.nih.gov/pubmed/4269800 PubMed].
** Inhibited by ATP (competitively) and f6p (non-competitively) in ''G. stearothermophillus'' [http://www.ncbi.nlm.nih.gov/pubmed/8136379 PubMed]
** Activated by GDP and ADP in lower concentrations (1mM); above that inhibition, competing with the ATP for the binding site (in ''G. stearothermophillus'') [http://www.ncbi.nlm.nih.gov/pubmed/7873536 PubMed]
** Activated by NH4+ [http://www.ncbi.nlm.nih.gov/pubmed/7873536 PubMed]

* '''Interactions:''' [[PfkA]]-[[Pgm]], [[PfkA]]-[[Eno]], [[PfkA]]-[[Rny]], [[PfkA]]-[[PnpA]], [[PfkA]]-[[RnjA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]

* '''Localization:''' cytoplasm (according to Swiss-Prot), Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1MTO 1MTO] (mutant, complex with fructose-6-phosphate, Geobacillus stearothermophilus), [http://www.rcsb.org/pdb/explore.do?structureId=4PFK 4PFK] (Geobacillus stearothermophilus), ''Geobacillus stearothermophilus'' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=58449 NCBI], Mutant form, complex with fructose-6-phosphate ''Geobacillus stearothermophilus'' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=21480 NCBI]

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O34529 O34529]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29190]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.1.11 2.7.1.11]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''pfkA [[pyk]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]

* '''Sigma factor:'''

* '''Regulation:''' twofold induced by glucose [http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:''' pGP393 (N-terminal His-tag, in [[pWH844]]), pGP87 (N-terminal Strep-tag, for [[SPINE]], expression in ''B. subtilis'', in [[pGP380]]), available in [[Stülke]] lab

* '''lacZ fusion:''' pGP511 (in [[pAC6]]), available in [[Stülke]] lab

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

[[Stülke|Jörg Stülke]], University of Göttingen, Germany [http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]

=Your additional remarks=

=References=

<pubmed> 16479537,19193632, 11489127, 8136379, 7873536 4269800 </pubmed>

Pyk

2009-06-11T10:59:04Z

Cadu Cunha: /* References */

* '''Description:''' pyruvate kinase, glycolytic enzyme <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pyk''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''pykA''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || pyruvate kinase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || catabolic enzyme in glycolysis
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 61,9 kDa, 4.88
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1755 bp, 585 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pfkA]]'', ''[[ytzA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14878]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:pyk_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29180

===Phenotypes of a mutant ===

Unable to grow with non-PTS carbohydrates (such as glucitol or glycerol) as single carbon source.

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pfkA-pyk-ytzA.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12661]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ADP + phosphoenolpyruvate --> ATP + pyruvate
** The reaction is irreversible under physiological conditions

* '''Protein family:''' PEP-utilizing enzyme family (according to Swiss-Prot) pyruvate kinase family, (C-terminal section: PEP-utilizing enzyme family)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Allosteric Regulation [http://www.ncbi.nlm.nih.gov/pubmed/3711058 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser36 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed], phosphorylation on Ser536 or Ser546 [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]

* '''Cofactor(s):''' Mg2+, K+

* '''Effectors of protein activity:'''
** Activated by PEP (Hill Coefficient 1,8) [http://www.ncbi.nlm.nih.gov/sites/entrez/4623707 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/3711058 PubMed]
** Allosterically activated by AMP [http://www.ncbi.nlm.nih.gov/pubmed/3711058 PubMed]
** Activation by r5p and ADP [http://www.ncbi.nlm.nih.gov/pubmed/3711058 PubMed]
** Inhibition by ADP and f16bp in high concentrations; and ATP [http://www.ncbi.nlm.nih.gov/pubmed/3711058 PubMed]

* '''Interactions:'''

* '''Localization:''' cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2E28 2E28] (Geobacillus stearothermophilus)

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P80885]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29180]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.1.40 2.7.1.40]

=== Additional information===
The enzyme is a tetramer with four active sites [http://www.ncbi.nlm.nih.gov/pubmed/3711058 PubMed]

=Expression and regulation=

* '''Operon:''' ''[[pfkA]] [[pyk]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]

* '''Sigma factor:'''

* '''Regulation:''' twofold induced by glucose [http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP590 (cat), available in [[Stülke]] lab

* '''Expression vector:'''
Expression in ''E. coli'', N-terminal His-tag: pGP1100 (in [[pWH844]]), available in [[Stülke]] lab

Expression in ''B. subtilis'', native protein: pGP1411 (in [[pBQ200]]), available in [[Stülke]] lab

Expression in ''B. subtilis'', N-terminal Strep-tag: pGP1409 (in [[pGP380]]), available in [[Stülke]] lab

Expression in ''B. subtilis'', C-terminal Strep-tag: pGP1410 (in [[pGP382]]), available in [[Stülke]] lab

* '''lacZ fusion:''' see ''[[pfkA]]''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

[[Stülke|Jörg Stülke]], University of Göttingen, Germany [http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]

=Your additional remarks=

=References=

<pubmed>17726680 16493705 11489127 17505547 10966427 17218307 3711058 4623707 </pubmed>
# Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in ''Bacillus subtilis''. ''Proteomics'' '''7:''' 3509-3526. [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
# Lévine et al. (2006) Analysis of the dynamic ''Bacillus subtilis'' Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. ''Proteomics'' '''6:''' 2157-2173 [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
# Ludwig, H., Homuth, G., Schmalisch, M., Dyka, F. M., Hecker, M., and Stülke, J. (2001) Transcription of glycolytic genes and operons in ''Bacillus subtilis'': evidence for the presence of multiple levels of control of the ''gapA'' operon. Mol Microbiol 41, 409-422.[http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]
# Jannière, L., Canceill, D., Suski, C., Kanga, S., Dalmais, B., Lestini, R., Monnier, A. F., Chapuis, J., Bolotin, A., Titok, M., Le Chatelier, E., and Ehrlich, S. D. (2007) Genetic evidence for a link between glycolysis and DNA replication. PLoS ONE 2, e447. [http://www.ncbi.nlm.nih.gov/sites/entrez/17505547 PubMed]
# Fry, B., Zhu, T., Domach, M. M., Koepsel, R. R., Phalakornkule, C., and Ataai, M. M. (2000) Characterization of growth and acid formation in a Bacillus subtilis pyruvate kinase mutant. Appl Env Microbiol 66: 4045-4049. [http://www.ncbi.nlm.nih.gov/sites/entrez/10966427 PubMed]
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]

YwlF

2009-06-11T10:56:15Z

Cadu Cunha: /* References */

* '''Description:''' ribose-5-phosphate isomerase <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ywlF''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ipc-32d ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || ribose-5-phosphate isomerase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || pentose phosphate pathway
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 16 kDa, 5.416
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 447 bp, 149 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywlG]]'', ''[[ywlE]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15709]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:ywlF_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU36920

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ywlFG.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10942]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:''' lacAB/rpiB family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Mass Action Kinetics [http://www.ncbi.nlm.nih.gov/sites/entrez/956158 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/7144591 PubMed]

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by 6-phosphogluconate and AMP [http://www.ncbi.nlm.nih.gov/sites/entrez/7144591 PubMed]
** Inhibited by divalent ions such as Ag2+, Mg2+, Co2+ and Zn2+ [http://www.ncbi.nlm.nih.gov/sites/entrez/956158 PubMed]
** Activated by EDTA and 2-mercaptoethanol [http://www.ncbi.nlm.nih.gov/sites/entrez/7144591 PubMed]

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39156 P39156]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU36920]

* '''E.C. number:''' [http://www.expasy.ch/cgi-bin/nicezyme.pl?5.3.1.6 5.3.1.6]

=== Additional information===
The enzyme has probably more than one active site, but with no cooperativity described [http://www.ncbi.nlm.nih.gov/sites/entrez/7144591 PubMed]

=Expression and regulation=

* '''Operon:'''

* '''[[Sigma factor]]:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed> 19446032 956158 7144591 956158</pubmed>
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

PdhD

2009-06-11T10:54:06Z

Cadu Cunha: /* Extended information on the protein */

* '''Description:''' dihydrolipoamide dehydrogenase E3 subunit of both pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase complexes <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pdhD''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citL ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || dihydrolipoamide dehydrogenase E3 subunit<br/> of both pyruvate dehydrogenase and 2-oxoglutarate<br/> dehydrogenase complexes
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || links glycolysis and TCA cycle, enzyme in TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 49 kDa, 4.76
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1410 bp, 470 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pdhC]]'', ''[[slp]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13334]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:pdhD_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/><br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU14610

===Phenotypes of a mutant ===

* defects in sporulation and unable to grow on glucose as single carbon source [http://www.ncbi.nlm.nih.gov/pubmed/11976308 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pdhABCD.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10210]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Protein N(6)-(dihydrolipoyl)lysine + NAD<sup>+</sup> = protein N(6)-(lipoyl)lysine + NADH (according to Swiss-Prot)

* '''Protein family:''' class-I pyridine nucleotide-disulfide oxidoreductase family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/6414463 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylated (Ser/Thr/Tyr) [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited thiamine 2-thiothiazolone diphosphate and NADH [http://www.ncbi.nlm.nih.gov/pubmed/6414463 PubMed]
** Low sensibility to NADPH [http://www.ncbi.nlm.nih.gov/pubmed/6414463 PubMed]

* '''Interactions:''' [[OdhA]]-[[OdhB]]-[[PdhD]], [[PdhA]]-[[PdhB]]-[[PdhC]]-[[PdhD]]

* '''Localization:''' cytoplasm (according to Swiss-Prot)

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1EBD 1EBD] (complex with binding domain of dihydrolipoamide acetylase, Geobacillus stearothermophilus), [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1EBD 1EBD] (complex with binding domain of dihydrolipoamide acetylase, ''Geobacillus stearothermophilus'')

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P21880 P21880]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14610]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.8.1.4 1.8.1.4]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[pdhA]]-[[pdhB]]-[[pdhC]]-[[pdhD]]''

* '''Sigma factor:''' [[SigA]]

* '''Regulation:''' expression activated by glucose (2.0 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>12850135 6414463 </pubmed>
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
# Gao et al. (2002) The E1beta and E2 subunits of the ''Bacillus subtilis'' pyruvate dehydrogenase complex are involved in regulation of sporulation.''J. Bacteriol.'' '''184:''' 2780-2788. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Icd

2009-06-11T10:52:13Z

Cadu Cunha: /* References */

* '''Description:''' isocitrate dehydrogenase <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''icd''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citC ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || isocitrate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46 kDa, 4.833
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1269 bp, 423 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[citZ]], [[mdh]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14873]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:icd_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29130

===Phenotypes of a mutant ===
reduced ability to sporulate [http://www.ncbi.nlm.nih.gov/pubmed/9244258 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10856]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Isocitrate + NADP<sup>+</sup> = 2-oxoglutarate + CO<sub>2</sub> + NADPH (according to Swiss-Prot)

* '''Protein family:''' isocitrate and isopropylmalate dehydrogenases family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/4147570 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylated [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]

* '''Cofactor(s):''' Mg2+, Mn2+

* '''Effectors of protein activity:'''
** Inhibited by glyoxylate, oxaloacetate and oxalomalate [http://www.ncbi.nlm.nih.gov/pubmed/4147570 PubMed]
*** Better inhibition when glyoxylate and oxaloacetate is combined, probably due to the non-enzymatic conversion into oxalomalate, which is a strong inhibitor [http://www.ncbi.nlm.nih.gov/pubmed/4147570 PubMed]

* '''Interactions:'''

* '''Localization:''' attached to the membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1HQS 1HQS]

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39126 P39126]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29130]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.42 1.1.1.42]

=== Additional information===
This enzyme requires NADP+ exclusively. No activity was seen on the presence on NAD+ [http://www.ncbi.nlm.nih.gov/pubmed/4147570 PubMed]

=Expression and regulation=

* '''Operon:'''
**''[[citZ]]-[[icd]]-[[mdh]]''
**''[[icd]]-[[mdh]]''

* '''Sigma factor:''' [[SigA]]

* '''Regulation:''' repressed by glucose (2.2-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed], ''[[citZ]]'': catabolite repression ([[CcpA]]), repression by glucose + glutamate ([[CcpC]])
''[[icd]]'': constitutive
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP666 (spc), GP672 (erm), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1121 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:''' available in [[Linc Sonenshein]] lab

=Labs working on this gene/protein=

[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

=Your additional remarks=

=References=

<pubmed>12850135 10348849 11751849 18763711 17726680 16493705 4147570 </pubmed>
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
# Matsuno K, Blais T, Serio AW, Conway T, Henkin TM, Sonenshein AL (1999) Metabolic imbalance and sporulation in an isocitrate dehydrogenase mutant of Bacillus subtilis. J Bacteriol 181:3382-3391. [http://www.ncbi.nlm.nih.gov/sites/entrez/10348849 PubMed]
# Singh SK, Miller SP, Dean A, Banaszak LJ, LaPorte DC (2002) Bacillus subtilis isocitrate dehydrogenase. A substrate analogue for Escherichia coli isocitrate dehydrogenase kinase/ phosphatase. J Biol Chem 277: 7567-7573. [http://www.ncbi.nlm.nih.gov/sites/entrez/11751849 PubMed]
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics 8: 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
# Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in ''Bacillus subtilis''. Proteomics 7: 3509-3526. [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
# Levine et al. (2006) Analysis of the dynamic ''Bacillus subtilis'' Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. Proteomics 6, 2157-2173. [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

CitZ

2009-06-11T10:51:04Z

Cadu Cunha: /* References */

* '''Description:''' citrate synthase <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citZ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citA2 ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || citrate synthase II
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 5.451
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1116 bp, 372 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytwI]], [[icd]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14874]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:citZ_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29140

===Phenotypes of a mutant ===
glutamate auxotrophy and a defect in sporulation [http://www.ncbi.nlm.nih.gov/pubmed/8045898 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10855]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Acetyl-CoA + H<sub>2</sub>O + oxaloacetate = citrate + CoA (according to Swiss-Prot)

* '''Protein family:''' citrate synthase family (according to Swiss-Prot)

* '''Paralogous protein(s):''' [[MmgD]], [[CitA]]

=== Extended information on the protein ===

* '''Kinetic information:''' Michaelis-Menten (Random Sequential Reaction Mechanism) [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-284 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by acetyl-CoA, 2-oxoglutarate and NADH [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]
** Inhibited by citrate and CoA (competitively against acetyl-CoA and non-competitively against oxaloacetate) [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
** Inhibited by ATP competitively in ''B. subtilis'' strain 168 and HS 1A17 [http://www.ncbi.nlm.nih.gov/sites/entrez/4980242 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
*** In ''B. subtilis'' strain HS 2A2, ATP inhibits a non-competitive fashion [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
** Activated by AMP [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2C6X 2C6X]

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39120 P39120]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29140]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.3.3.1 2.3.3.1]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[citZ]]-[[icd]]-[[mdh]]''

* '''Sigma factor:''' [[SigA]]

* '''Regulation:''' repressed by glucose (6.7-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed], catabolite repression ([[CcpA]]), repression by glucose + glutamate ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed], repression under anaerobic conditions [http://www.ncbi.nlm.nih.gov/pubmed/9642180 PubMed]

* '''Regulatory mechanism:''' [[CcpA]]: transcription repression, [[CcpA]]: transcription repression, [[CcpC]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP678 (erm), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1120 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:''' available in [[Linc Sonenshein]] lab

=Labs working on this gene/protein=

[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

[[Stülke|Jörg Stülke]], University of Göttingen, Germany
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]

=Your additional remarks=

=References=

<pubmed>12850135 17218307 12100558 9642180 8045898 8655569 4211224 4980242 </pubmed>
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
# Kim HJ, Roux A, Sonenshein AL (2002b) Direct and indirect roles of CcpA in regulation of ''Bacillus subtilis'' Krebs cycle genes. Mol Microbiol 45:179-190. [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]
# Nakano MM, Zuber P, Sonenshein AL (1998) Anaerobic regulation of ''Bacillus subtilis'' Krebs cycle genes. ''J Bacteriol.'' '''180:''' 3304-3311. [http://www.ncbi.nlm.nih.gov/pubmed/9642180 PubMed]
# Jin S, Sonenshein AL (1994) Identification of two distinct ''Bacillus subtilis'' citrate synthase genes ''J Bacteriol.'' '''176:''' 4669-4679. [http://www.ncbi.nlm.nih.gov/pubmed/8045898 PubMed]
# Danson MJ et al. (1984) Citric acid cycle enzymes of the archaebacteria: citrate synthase and succinate thiokinase. ''FEBS Letters''. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

SucC

2009-06-11T10:49:01Z

Cadu Cunha: /* References */

* '''Description:''' succinyl-CoA synthetase (beta subunit) <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sucC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || succinyl-CoA synthetase (beta subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 4.846
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1155 bp, 385 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ylqH]], [[sucD]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13482]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:sucC_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16090

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sucCD.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12680]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + succinate + CoA = ADP + phosphate + succinyl-CoA (according to Swiss-Prot)

* '''Protein family:''' ATP-grasp domain (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-220 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by 2-oxoglutarate, ATP and NADH [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]
*** GTP is not accept by the enzyme [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1JKJ 1JKJ] (E. coli)

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P80886 P80886]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16090]

* '''E.C. number:''' [http://www.expasy.org/enzyme/6.2.1.5 6.2.1.5]

=== Additional information===
The enzyme is a dimer [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]

=Expression and regulation=

* '''Operon:''' ''[[sucC]]''-''[[SucD]]''

* '''Sigma factor:'''

* '''Regulation:''' repressed by glucose (2.7-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]

* '''Regulatory mechanism:''' [[CcpA]]: transcription repression

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>12850135 17218307 17218307 </pubmed>

# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
# Danson MJ et al. (1984) Citric acid cycle enzymes of the archaebacteria: citrate synthase and succinate thiokinase. ''FEBS Letters''. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

SucC

2009-06-11T10:48:40Z

Cadu Cunha: /* References */

* '''Description:''' succinyl-CoA synthetase (beta subunit) <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sucC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || succinyl-CoA synthetase (beta subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 4.846
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1155 bp, 385 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ylqH]], [[sucD]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13482]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:sucC_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16090

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sucCD.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12680]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + succinate + CoA = ADP + phosphate + succinyl-CoA (according to Swiss-Prot)

* '''Protein family:''' ATP-grasp domain (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-220 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by 2-oxoglutarate, ATP and NADH [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]
*** GTP is not accept by the enzyme [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1JKJ 1JKJ] (E. coli)

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P80886 P80886]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16090]

* '''E.C. number:''' [http://www.expasy.org/enzyme/6.2.1.5 6.2.1.5]

=== Additional information===
The enzyme is a dimer [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]

=Expression and regulation=

* '''Operon:''' ''[[sucC]]''-''[[SucD]]''

* '''Sigma factor:'''

* '''Regulation:''' repressed by glucose (2.7-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]

* '''Regulatory mechanism:''' [[CcpA]]: transcription repression

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>12850135 17218307 17218307 </pubmed>
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]

# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]

# Danson MJ et al. (1984) Citric acid cycle enzymes of the archaebacteria: citrate synthase and succinate thiokinase. ''FEBS Letters''. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

SucD

2009-06-11T10:48:23Z

Cadu Cunha: /* References */

* '''Description:''' succinyl-CoA synthetase (alpha subunit) <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sucD''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || succinyl-CoA synthetase (alpha subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 31 kDa, 5.587
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 900 bp, 300 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sucC]], [[smf]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13483]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:sucD_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16100

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sucCD.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12681]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + succinate + CoA = ADP + phosphate + succinyl-CoA (according to Swiss-Prot)

* '''Protein family:''' succinate/malate CoA ligase alpha subunit family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]

* '''Domains:'''

* '''Modification:''' phosphorylation on (Ser-19 OR Thr-20) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by 2-oxoglutarate, ATP and NADH [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]
*** GTP is not accept by the enzyme [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1JKJ 1JKJ] (E. coli)

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P80865 P80865]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16100]

* '''E.C. number:''' [http://www.expasy.org/enzyme/6.2.1.5 6.2.1.5]

=== Additional information===
The enzyme is a dimer [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]

=Expression and regulation=

* '''Operon:''' ''[[sucC]]''-''[[SucD]]''

* '''Sigma factor:'''

* '''Regulation:''' repressed by glucose (2.4-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]

* '''Regulatory mechanism:''' [[CcpA]]: transcription repression

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP720 (spc), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>12850135 17218307 17218307 </pubmed>
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
# Danson MJ et al. (1984) Citric acid cycle enzymes of the archaebacteria: citrate synthase and succinate thiokinase. ''FEBS Letters''. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

SucC

2009-06-11T10:47:58Z

Cadu Cunha: /* References */

* '''Description:''' succinyl-CoA synthetase (beta subunit) <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sucC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || succinyl-CoA synthetase (beta subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 4.846
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1155 bp, 385 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ylqH]], [[sucD]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13482]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:sucC_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16090

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sucCD.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12680]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + succinate + CoA = ADP + phosphate + succinyl-CoA (according to Swiss-Prot)

* '''Protein family:''' ATP-grasp domain (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-220 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by 2-oxoglutarate, ATP and NADH [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]
*** GTP is not accept by the enzyme [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1JKJ 1JKJ] (E. coli)

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P80886 P80886]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16090]

* '''E.C. number:''' [http://www.expasy.org/enzyme/6.2.1.5 6.2.1.5]

=== Additional information===
The enzyme is a dimer [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]

=Expression and regulation=

* '''Operon:''' ''[[sucC]]''-''[[SucD]]''

* '''Sigma factor:'''

* '''Regulation:''' repressed by glucose (2.7-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]

* '''Regulatory mechanism:''' [[CcpA]]: transcription repression

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>12850135 17218307 17218307 </pubmed>
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
# Danson MJ et al. (1984) Citric acid cycle enzymes of the archaebacteria: citrate synthase and succinate thiokinase. ''FEBS Letters''. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

SdhB

2009-06-11T10:43:21Z

Cadu Cunha: /* References */

* '''Description:''' succinate dehydrogenase <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sdhB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || succinate dehydrogenase (iron-sulfur protein)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 7.989
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 759 bp, 253 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sdhA]], [[ysmA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14803]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:sdhB_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU28430

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sdhCAB.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10353]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Succinate + acceptor = fumarate + reduced acceptor (according to Swiss-Prot)

* '''Protein family:''' succinate dehydrogenase/fumarate reductase iron-sulfur protein family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):''' Fe

* '''Effectors of protein activity:'''
** Inhibited by 2-(n-Heptyl)-4-hydroxy-quinoline N-oxide [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed]
** Activated by Cytochrome b558 [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]

* '''Interactions:''' [[SdhA]]-[[SdhB]]-[[SdhC]]

* '''Localization:''' attached to the membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NEK 1NEK] (''E. coli'')

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P08066 P08066]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28430]

* '''E.C. number:'''EC 1.3.99.1

=== Additional information===
This enzyme is a trimer membrane-bound [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* One subunit is bound to citochrome b558, and this subunit is the one bound to the cytosolic side of the membrane [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* Another subunit is the flavoprotein one, required for FAD usage [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* The other subunit has an iron-sulphur domain necessary for the catalytic activity [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]

=Expression and regulation=

* '''Operon:''' ''[[sdhC]]''-''[[sdhA]]''-''[[sdhB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/3036777 PubMed]

* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2495271 PubMed]

* '''Regulation:''' constitutive

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed> 3910107 6799760 </pubmed>
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics 8: 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

SdhA

2009-06-11T10:42:53Z

Cadu Cunha: /* References */

* '''Description:''' succinate dehydrogenase (flavoprotein subunit) <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sdhA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citF ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || succinate dehydrogenase (flavoprotein subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 65 kDa, 5.714
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1758 bp, 586 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sdhC]], [[sdhB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14804]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:sdhA_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU28440

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sdhCAB.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10352]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Succinate + acceptor = fumarate + reduced acceptor (according to Swiss-Prot)

* '''Protein family:''' FRD/SDH subfamily (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylated [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]

* '''Cofactor(s):''' Fe

* '''Effectors of protein activity:'''
** Inhibited by 2-(n-Heptyl)-4-hydroxy-quinoline N-oxide [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed]
** Activated by Cytochrome b558 [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]

* '''Interactions:''' [[SdhA]]-[[SdhB]]-[[SdhC]]

* '''Localization:''' membrane protein [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NEK 1NEK] (''E. coli'')

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P08065 P08065]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28440]

* '''E.C. number:''' 1.3.99.1

=== Additional information===
This enzyme is a trimer membrane-bound [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* One subunit is bound to citochrome b558, and this subunit is the one bound to the cytosolic side of the membrane [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* Another subunit is the flavoprotein one, required for FAD usage [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* The other subunit has an iron-sulphur domain necessary for the catalytic activity [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]

=Expression and regulation=

* '''Operon:''' ''[[sdhC]]''-''[[sdhA]]''-''[[sdhB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/3036777 PubMed]

* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2495271 PubMed]

* '''Regulation:''' constitutive

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP743 (''sdhCA'', cat), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>17726680 18763711 17726680 16493705 3910107 6799760 </pubmed>
# Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in ''Bacillus subtilis''. ''Proteomics'' '''7:''' 3509-3526. [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics '''8:''' 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]# Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in ''Bacillus subtilis''. Proteomics 7: 3509-3526. [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
# Levine et al. (2006) Analysis of the dynamic ''Bacillus subtilis'' Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. Proteomics 6, 2157-2173. [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

SdhC

2009-06-11T10:42:13Z

Cadu Cunha: /* References */

* '''Description:''' succinate dehydrogenase(cytochrome b558 subunit) <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sdhC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || succinate dehydrogenase (cytochrome b558 subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 9.831
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 606 bp, 202 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yslB]], [[sdhA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14805]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:sdhC_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU28450

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sdhCAB.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10351]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:''' cytochrome b558 family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''
* '''Cofactor(s):''' Fe

* '''Effectors of protein activity:'''
** Inhibited by 2-(n-Heptyl)-4-hydroxy-quinoline N-oxide [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed]
** Activated by Cytochrome b558 [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]

* '''Interactions:''' [[SdhA]]-[[SdhB]]-[[SdhC]]

* '''Localization:''' cell membrane (according to Swiss-Prot), membrane protein [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NEK 1NEK] (''E. coli'')

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P08064 P08064]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28450]

* '''E.C. number:''' 1.3.99.1

=== Additional information===
This enzyme is a trimer membrane-bound [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* One subunit is bound to citochrome b558, and this subunit is the one bound to the cytosolic side of the membrane [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* Another subunit is the flavoprotein one, required for FAD usage [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* The other subunit has an iron-sulphur domain necessary for the catalytic activity [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]

=Expression and regulation=

* '''Operon:''' ''[[sdhC]]''-''[[sdhA]]''-''[[sdhB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/3036777 PubMed]

* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2495271 PubMed]

* '''Regulation:''' SdhC is less expressed under conditions of extreme iron starvation ([[FsrA]]) [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]

* '''Regulatory mechanism:''' [[FsrA]]: translational repression, [[sRNA]] [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP743 (''sdhCA'', cat), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>18763711 18697947 3910107 6799760 </pubmed>
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics '''8:''' 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
# Gaballa A, Antelmann H, Aguilar C, Khakh SK, Song KB, Smaldone GT, Helmann JD (2008) The Bacillus subtilis iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins. PNAS 105: 11927-11932. [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Mdh

2009-06-11T10:40:19Z

Cadu Cunha: /* References */

* '''Description:''' malate dehydrogenase <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''mdh''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citH ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || malate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 4.727
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 936 bp, 312 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[icd]], [[phoP]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14872]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:mdh_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/><br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29120

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11386]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' (S)-malate + NAD<sup>+</sup> = oxaloacetate + NADH (according to Swiss-Prot)

* '''Protein family:''' MDH type 3 family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by Mg2+, Ca2+, Zn2+, Ag2+ and Hg2+ [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/922015 PubMed]
** Inhibited by oxaloacetate (above 1mM) and malate (above 7,7mM) [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

* '''Interactions:'''

* '''Localization:''' cytoplasm (according to Swiss-Prot), membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1EMD 1EMD] (''E.coli'')

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P49814 P49814]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29120]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.37 1.1.1.37]

=== Additional information===
The enzyme is a tetramer [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

=Expression and regulation=
* '''Operon:'''
**''[[citZ]]-[[icd]]-[[mdh]]''
**''[[icd]]-[[mdh]]''

* '''Sigma factor:''' [[SigA]]

* '''Regulation:''' ''[[citZ]]'': catabolite repression ([[CcpA]]), repression by glucose + glutamate ([[CcpC]])
''[[mdh]]'': constitutive
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression, [[CcpC]]: transcription repression

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP719 (spc), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1123 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>18763711 14284712 922015 </pubmed>
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics '''8:''' 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Mdh

2009-06-10T16:46:21Z

Cadu Cunha: /* Additional information */

* '''Description:''' malate dehydrogenase <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''mdh''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citH ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || malate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 4.727
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 936 bp, 312 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[icd]], [[phoP]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14872]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:mdh_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/><br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29120

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11386]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' (S)-malate + NAD<sup>+</sup> = oxaloacetate + NADH (according to Swiss-Prot)

* '''Protein family:''' MDH type 3 family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by Mg2+, Ca2+, Zn2+, Ag2+ and Hg2+ [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/922015 PubMed]
** Inhibited by oxaloacetate (above 1mM) and malate (above 7,7mM) [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

* '''Interactions:'''

* '''Localization:''' cytoplasm (according to Swiss-Prot), membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1EMD 1EMD] (''E.coli'')

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P49814 P49814]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29120]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.37 1.1.1.37]

=== Additional information===
The enzyme is a tetramer [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

=Expression and regulation=
* '''Operon:'''
**''[[citZ]]-[[icd]]-[[mdh]]''
**''[[icd]]-[[mdh]]''

* '''Sigma factor:''' [[SigA]]

* '''Regulation:''' ''[[citZ]]'': catabolite repression ([[CcpA]]), repression by glucose + glutamate ([[CcpC]])
''[[mdh]]'': constitutive
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression, [[CcpC]]: transcription repression

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP719 (spc), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1123 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>18763711, </pubmed>
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics '''8:''' 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Mdh

2009-06-10T16:45:01Z

Cadu Cunha: /* The protein */

* '''Description:''' malate dehydrogenase <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''mdh''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citH ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || malate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 4.727
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 936 bp, 312 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[icd]], [[phoP]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14872]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:mdh_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/><br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29120

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11386]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' (S)-malate + NAD<sup>+</sup> = oxaloacetate + NADH (according to Swiss-Prot)

* '''Protein family:''' MDH type 3 family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by Mg2+, Ca2+, Zn2+, Ag2+ and Hg2+ [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/922015 PubMed]
** Inhibited by oxaloacetate (above 1mM) and malate (above 7,7mM) [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

* '''Interactions:'''

* '''Localization:''' cytoplasm (according to Swiss-Prot), membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1EMD 1EMD] (''E.coli'')

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P49814 P49814]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29120]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.37 1.1.1.37]

=== Additional information===

=Expression and regulation=
* '''Operon:'''
**''[[citZ]]-[[icd]]-[[mdh]]''
**''[[icd]]-[[mdh]]''

* '''Sigma factor:''' [[SigA]]

* '''Regulation:''' ''[[citZ]]'': catabolite repression ([[CcpA]]), repression by glucose + glutamate ([[CcpC]])
''[[mdh]]'': constitutive
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression, [[CcpC]]: transcription repression

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP719 (spc), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1123 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>18763711, </pubmed>
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics '''8:''' 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Mdh

2009-06-10T16:43:31Z

Cadu Cunha: /* Extended information on the protein */

* '''Description:''' malate dehydrogenase <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''mdh''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citH ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || malate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 4.727
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 936 bp, 312 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[icd]], [[phoP]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14872]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:mdh_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/><br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29120

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11386]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' (S)-malate + NAD<sup>+</sup> = oxaloacetate + NADH (according to Swiss-Prot)

* '''Protein family:''' MDH type 3 family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by Mg2+, Ca2+, Zn2+, Ag2+ and Hg2+ [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/922015 PubMed]
** Inhibited by oxaloacetate (above 1mM) and malate (above 7,7mM) [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]

* '''Interactions:'''

* '''Localization:''' cytoplasm (according to Swiss-Prot), membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1EMD 1EMD] (''E.coli'')

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P49814 P49814]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29120]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.37 1.1.1.37]

=== Additional information===

* '''Operon:'''
**''[[citZ]]-[[icd]]-[[mdh]]''
**''[[icd]]-[[mdh]]''

* '''Sigma factor:''' [[SigA]]

* '''Regulation:''' ''[[citZ]]'': catabolite repression ([[CcpA]]), repression by glucose + glutamate ([[CcpC]])
''[[mdh]]'': constitutive
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression, [[CcpC]]: transcription repression

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP719 (spc), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1123 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>18763711, </pubmed>
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics '''8:''' 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Mdh

2009-06-10T16:34:51Z

Cadu Cunha: /* Database entries */

* '''Description:''' malate dehydrogenase <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''mdh''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citH ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || malate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 4.727
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 936 bp, 312 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[icd]], [[phoP]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14872]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:mdh_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/><br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29120

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11386]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' (S)-malate + NAD<sup>+</sup> = oxaloacetate + NADH (according to Swiss-Prot)

* '''Protein family:''' MDH type 3 family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:'''

* '''Localization:''' cytoplasm (according to Swiss-Prot), membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1EMD 1EMD] (''E.coli'')

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P49814 P49814]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29120]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.37 1.1.1.37]

=== Additional information===

* '''Operon:'''
**''[[citZ]]-[[icd]]-[[mdh]]''
**''[[icd]]-[[mdh]]''

* '''Sigma factor:''' [[SigA]]

* '''Regulation:''' ''[[citZ]]'': catabolite repression ([[CcpA]]), repression by glucose + glutamate ([[CcpC]])
''[[mdh]]'': constitutive
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression, [[CcpC]]: transcription repression

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP719 (spc), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1123 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>18763711, </pubmed>
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics '''8:''' 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

SdhC

2009-06-10T16:24:24Z

Cadu Cunha: /* Extended information on the protein */

* '''Description:''' succinate dehydrogenase(cytochrome b558 subunit) <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sdhC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || succinate dehydrogenase (cytochrome b558 subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 9.831
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 606 bp, 202 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yslB]], [[sdhA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14805]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:sdhC_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU28450

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sdhCAB.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10351]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:''' cytochrome b558 family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''
* '''Cofactor(s):''' Fe

* '''Effectors of protein activity:'''
** Inhibited by 2-(n-Heptyl)-4-hydroxy-quinoline N-oxide [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed]
** Activated by Cytochrome b558 [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]

* '''Interactions:''' [[SdhA]]-[[SdhB]]-[[SdhC]]

* '''Localization:''' cell membrane (according to Swiss-Prot), membrane protein [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NEK 1NEK] (''E. coli'')

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P08064 P08064]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28450]

* '''E.C. number:''' 1.3.99.1

=== Additional information===
This enzyme is a trimer membrane-bound [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* One subunit is bound to citochrome b558, and this subunit is the one bound to the cytosolic side of the membrane [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* Another subunit is the flavoprotein one, required for FAD usage [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* The other subunit has an iron-sulphur domain necessary for the catalytic activity [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]

=Expression and regulation=

* '''Operon:''' ''[[sdhC]]''-''[[sdhA]]''-''[[sdhB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/3036777 PubMed]

* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2495271 PubMed]

* '''Regulation:''' SdhC is less expressed under conditions of extreme iron starvation ([[FsrA]]) [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]

* '''Regulatory mechanism:''' [[FsrA]]: translational repression, [[sRNA]] [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP743 (''sdhCA'', cat), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>18763711 18697947, </pubmed>
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics '''8:''' 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
# Gaballa A, Antelmann H, Aguilar C, Khakh SK, Song KB, Smaldone GT, Helmann JD (2008) The Bacillus subtilis iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins. PNAS 105: 11927-11932. [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

SdhA

2009-06-10T16:24:10Z

Cadu Cunha: /* Extended information on the protein */

* '''Description:''' succinate dehydrogenase (flavoprotein subunit) <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sdhA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citF ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || succinate dehydrogenase (flavoprotein subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 65 kDa, 5.714
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1758 bp, 586 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sdhC]], [[sdhB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14804]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:sdhA_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU28440

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sdhCAB.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10352]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Succinate + acceptor = fumarate + reduced acceptor (according to Swiss-Prot)

* '''Protein family:''' FRD/SDH subfamily (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylated [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]

* '''Cofactor(s):''' Fe

* '''Effectors of protein activity:'''
** Inhibited by 2-(n-Heptyl)-4-hydroxy-quinoline N-oxide [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed]
** Activated by Cytochrome b558 [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]

* '''Interactions:''' [[SdhA]]-[[SdhB]]-[[SdhC]]

* '''Localization:''' membrane protein [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NEK 1NEK] (''E. coli'')

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P08065 P08065]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28440]

* '''E.C. number:''' 1.3.99.1

=== Additional information===
This enzyme is a trimer membrane-bound [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* One subunit is bound to citochrome b558, and this subunit is the one bound to the cytosolic side of the membrane [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* Another subunit is the flavoprotein one, required for FAD usage [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* The other subunit has an iron-sulphur domain necessary for the catalytic activity [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]

=Expression and regulation=

* '''Operon:''' ''[[sdhC]]''-''[[sdhA]]''-''[[sdhB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/3036777 PubMed]

* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2495271 PubMed]

* '''Regulation:''' constitutive

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP743 (''sdhCA'', cat), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>17726680 18763711 17726680 16493705, </pubmed>
# Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in ''Bacillus subtilis''. ''Proteomics'' '''7:''' 3509-3526. [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics '''8:''' 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]# Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in ''Bacillus subtilis''. Proteomics 7: 3509-3526. [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
# Levine et al. (2006) Analysis of the dynamic ''Bacillus subtilis'' Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. Proteomics 6, 2157-2173. [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

SdhB

2009-06-10T16:23:23Z

Cadu Cunha: /* Extended information on the protein */

* '''Description:''' succinate dehydrogenase <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sdhB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || succinate dehydrogenase (iron-sulfur protein)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 7.989
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 759 bp, 253 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sdhA]], [[ysmA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14803]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:sdhB_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU28430

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sdhCAB.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10353]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Succinate + acceptor = fumarate + reduced acceptor (according to Swiss-Prot)

* '''Protein family:''' succinate dehydrogenase/fumarate reductase iron-sulfur protein family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):''' Fe

* '''Effectors of protein activity:'''
** Inhibited by 2-(n-Heptyl)-4-hydroxy-quinoline N-oxide [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed]
** Activated by Cytochrome b558 [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]

* '''Interactions:''' [[SdhA]]-[[SdhB]]-[[SdhC]]

* '''Localization:''' attached to the membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NEK 1NEK] (''E. coli'')

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P08066 P08066]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28430]

* '''E.C. number:'''EC 1.3.99.1

=== Additional information===
This enzyme is a trimer membrane-bound [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* One subunit is bound to citochrome b558, and this subunit is the one bound to the cytosolic side of the membrane [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* Another subunit is the flavoprotein one, required for FAD usage [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* The other subunit has an iron-sulphur domain necessary for the catalytic activity [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]

=Expression and regulation=

* '''Operon:''' ''[[sdhC]]''-''[[sdhA]]''-''[[sdhB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/3036777 PubMed]

* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2495271 PubMed]

* '''Regulation:''' constitutive

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics 8: 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

SdhC

2009-06-10T16:20:15Z

Cadu Cunha: /* Additional information */

* '''Description:''' succinate dehydrogenase(cytochrome b558 subunit) <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sdhC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || succinate dehydrogenase (cytochrome b558 subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 9.831
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 606 bp, 202 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yslB]], [[sdhA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14805]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:sdhC_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU28450

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sdhCAB.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10351]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:''' cytochrome b558 family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:''' [[SdhA]]-[[SdhB]]-[[SdhC]]

* '''Localization:''' cell membrane (according to Swiss-Prot), membrane protein [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NEK 1NEK] (''E. coli'')

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P08064 P08064]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28450]

* '''E.C. number:''' 1.3.99.1

=== Additional information===
This enzyme is a trimer membrane-bound [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* One subunit is bound to citochrome b558, and this subunit is the one bound to the cytosolic side of the membrane [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* Another subunit is the flavoprotein one, required for FAD usage [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* The other subunit has an iron-sulphur domain necessary for the catalytic activity [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]

=Expression and regulation=

* '''Operon:''' ''[[sdhC]]''-''[[sdhA]]''-''[[sdhB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/3036777 PubMed]

* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2495271 PubMed]

* '''Regulation:''' SdhC is less expressed under conditions of extreme iron starvation ([[FsrA]]) [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]

* '''Regulatory mechanism:''' [[FsrA]]: translational repression, [[sRNA]] [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP743 (''sdhCA'', cat), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>18763711 18697947, </pubmed>
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics '''8:''' 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
# Gaballa A, Antelmann H, Aguilar C, Khakh SK, Song KB, Smaldone GT, Helmann JD (2008) The Bacillus subtilis iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins. PNAS 105: 11927-11932. [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

SdhC

2009-06-10T16:20:04Z

Cadu Cunha: /* Additional information */

* '''Description:''' succinate dehydrogenase(cytochrome b558 subunit) <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sdhC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || succinate dehydrogenase (cytochrome b558 subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 9.831
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 606 bp, 202 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yslB]], [[sdhA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14805]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:sdhC_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU28450

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sdhCAB.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10351]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:''' cytochrome b558 family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:''' [[SdhA]]-[[SdhB]]-[[SdhC]]

* '''Localization:''' cell membrane (according to Swiss-Prot), membrane protein [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NEK 1NEK] (''E. coli'')

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P08064 P08064]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28450]

* '''E.C. number:''' 1.3.99.1

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[sdhC]]''-''[[sdhA]]''-''[[sdhB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/3036777 PubMed]

* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2495271 PubMed]

* '''Regulation:''' SdhC is less expressed under conditions of extreme iron starvation ([[FsrA]]) [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]

* '''Regulatory mechanism:''' [[FsrA]]: translational repression, [[sRNA]] [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP743 (''sdhCA'', cat), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>18763711 18697947, </pubmed>
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics '''8:''' 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
# Gaballa A, Antelmann H, Aguilar C, Khakh SK, Song KB, Smaldone GT, Helmann JD (2008) The Bacillus subtilis iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins. PNAS 105: 11927-11932. [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

SdhC

2009-06-10T16:19:48Z

Cadu Cunha: /* Additional information */

* '''Description:''' succinate dehydrogenase(cytochrome b558 subunit) <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sdhC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || succinate dehydrogenase (cytochrome b558 subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 9.831
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 606 bp, 202 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yslB]], [[sdhA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14805]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:sdhC_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU28450

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sdhCAB.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10351]

=== Additional information===
This enzyme is a trimer membrane-bound [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* One subunit is bound to citochrome b558, and this subunit is the one bound to the cytosolic side of the membrane [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* Another subunit is the flavoprotein one, required for FAD usage [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* The other subunit has an iron-sulphur domain necessary for the catalytic activity [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:''' cytochrome b558 family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:''' [[SdhA]]-[[SdhB]]-[[SdhC]]

* '''Localization:''' cell membrane (according to Swiss-Prot), membrane protein [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NEK 1NEK] (''E. coli'')

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P08064 P08064]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28450]

* '''E.C. number:''' 1.3.99.1

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[sdhC]]''-''[[sdhA]]''-''[[sdhB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/3036777 PubMed]

* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2495271 PubMed]

* '''Regulation:''' SdhC is less expressed under conditions of extreme iron starvation ([[FsrA]]) [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]

* '''Regulatory mechanism:''' [[FsrA]]: translational repression, [[sRNA]] [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP743 (''sdhCA'', cat), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>18763711 18697947, </pubmed>
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics '''8:''' 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
# Gaballa A, Antelmann H, Aguilar C, Khakh SK, Song KB, Smaldone GT, Helmann JD (2008) The Bacillus subtilis iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins. PNAS 105: 11927-11932. [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

SdhA

2009-06-10T16:19:40Z

Cadu Cunha: /* Additional information */

* '''Description:''' succinate dehydrogenase (flavoprotein subunit) <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sdhA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citF ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || succinate dehydrogenase (flavoprotein subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 65 kDa, 5.714
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1758 bp, 586 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sdhC]], [[sdhB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14804]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:sdhA_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU28440

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sdhCAB.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10352]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Succinate + acceptor = fumarate + reduced acceptor (according to Swiss-Prot)

* '''Protein family:''' FRD/SDH subfamily (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylated [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:''' [[SdhA]]-[[SdhB]]-[[SdhC]]

* '''Localization:''' membrane protein [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NEK 1NEK] (''E. coli'')

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P08065 P08065]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28440]

* '''E.C. number:''' 1.3.99.1

=== Additional information===
This enzyme is a trimer membrane-bound [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* One subunit is bound to citochrome b558, and this subunit is the one bound to the cytosolic side of the membrane [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* Another subunit is the flavoprotein one, required for FAD usage [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* The other subunit has an iron-sulphur domain necessary for the catalytic activity [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]

=Expression and regulation=

* '''Operon:''' ''[[sdhC]]''-''[[sdhA]]''-''[[sdhB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/3036777 PubMed]

* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2495271 PubMed]

* '''Regulation:''' constitutive

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP743 (''sdhCA'', cat), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>17726680 18763711 17726680 16493705, </pubmed>
# Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in ''Bacillus subtilis''. ''Proteomics'' '''7:''' 3509-3526. [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics '''8:''' 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]# Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in ''Bacillus subtilis''. Proteomics 7: 3509-3526. [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
# Levine et al. (2006) Analysis of the dynamic ''Bacillus subtilis'' Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. Proteomics 6, 2157-2173. [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

SdhB

2009-06-10T16:19:18Z

Cadu Cunha: /* Additional information */

* '''Description:''' succinate dehydrogenase <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sdhB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || succinate dehydrogenase (iron-sulfur protein)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 7.989
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 759 bp, 253 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sdhA]], [[ysmA]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14803]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:sdhB_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU28430

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sdhCAB.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10353]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Succinate + acceptor = fumarate + reduced acceptor (according to Swiss-Prot)

* '''Protein family:''' succinate dehydrogenase/fumarate reductase iron-sulfur protein family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:''' [[SdhA]]-[[SdhB]]-[[SdhC]]

* '''Localization:''' attached to the membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NEK 1NEK] (''E. coli'')

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P08066 P08066]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28430]

* '''E.C. number:'''EC 1.3.99.1

=== Additional information===
This enzyme is a trimer membrane-bound [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* One subunit is bound to citochrome b558, and this subunit is the one bound to the cytosolic side of the membrane [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* Another subunit is the flavoprotein one, required for FAD usage [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]
* The other subunit has an iron-sulphur domain necessary for the catalytic activity [http://www.ncbi.nlm.nih.gov/pubmed/3910107 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/6799760 PubMed]

=Expression and regulation=

* '''Operon:''' ''[[sdhC]]''-''[[sdhA]]''-''[[sdhB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/3036777 PubMed]

* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2495271 PubMed]

* '''Regulation:''' constitutive

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics 8: 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

SucC

2009-06-10T15:53:24Z

Cadu Cunha: /* Additional information */

* '''Description:''' succinyl-CoA synthetase (beta subunit) <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sucC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || succinyl-CoA synthetase (beta subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 4.846
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1155 bp, 385 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ylqH]], [[sucD]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13482]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:sucC_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16090

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sucCD.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12680]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + succinate + CoA = ADP + phosphate + succinyl-CoA (according to Swiss-Prot)

* '''Protein family:''' ATP-grasp domain (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-220 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by 2-oxoglutarate, ATP and NADH [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]
*** GTP is not accept by the enzyme [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1JKJ 1JKJ] (E. coli)

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P80886 P80886]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16090]

* '''E.C. number:''' [http://www.expasy.org/enzyme/6.2.1.5 6.2.1.5]

=== Additional information===
The enzyme is a dimer [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]

=Expression and regulation=

* '''Operon:''' ''[[sucC]]''-''[[SucD]]''

* '''Sigma factor:'''

* '''Regulation:''' repressed by glucose (2.7-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]

* '''Regulatory mechanism:''' [[CcpA]]: transcription repression

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>12850135 17218307, </pubmed>
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

SucC

2009-06-10T15:53:05Z

Cadu Cunha: /* Extended information on the protein */

* '''Description:''' succinyl-CoA synthetase (beta subunit) <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sucC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || succinyl-CoA synthetase (beta subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 4.846
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1155 bp, 385 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ylqH]], [[sucD]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13482]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:sucC_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16090

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sucCD.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12680]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + succinate + CoA = ADP + phosphate + succinyl-CoA (according to Swiss-Prot)

* '''Protein family:''' ATP-grasp domain (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-220 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by 2-oxoglutarate, ATP and NADH [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]
*** GTP is not accept by the enzyme [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1JKJ 1JKJ] (E. coli)

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P80886 P80886]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16090]

* '''E.C. number:''' [http://www.expasy.org/enzyme/6.2.1.5 6.2.1.5]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[sucC]]''-''[[SucD]]''

* '''Sigma factor:'''

* '''Regulation:''' repressed by glucose (2.7-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]

* '''Regulatory mechanism:''' [[CcpA]]: transcription repression

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>12850135 17218307, </pubmed>
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

SucD

2009-06-10T15:52:28Z

Cadu Cunha: /* Additional information */

* '''Description:''' succinyl-CoA synthetase (alpha subunit) <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sucD''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || succinyl-CoA synthetase (alpha subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 31 kDa, 5.587
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 900 bp, 300 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sucC]], [[smf]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13483]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:sucD_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16100

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sucCD.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12681]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + succinate + CoA = ADP + phosphate + succinyl-CoA (according to Swiss-Prot)

* '''Protein family:''' succinate/malate CoA ligase alpha subunit family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]

* '''Domains:'''

* '''Modification:''' phosphorylation on (Ser-19 OR Thr-20) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by 2-oxoglutarate, ATP and NADH [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]
*** GTP is not accept by the enzyme [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1JKJ 1JKJ] (E. coli)

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P80865 P80865]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16100]

* '''E.C. number:''' [http://www.expasy.org/enzyme/6.2.1.5 6.2.1.5]

=== Additional information===
The enzyme is a dimer [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]

=Expression and regulation=

* '''Operon:''' ''[[sucC]]''-''[[SucD]]''

* '''Sigma factor:'''

* '''Regulation:''' repressed by glucose (2.4-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]

* '''Regulatory mechanism:''' [[CcpA]]: transcription repression

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP720 (spc), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>12850135 17218307, </pubmed>
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

SucD

2009-06-10T15:51:47Z

Cadu Cunha: /* Extended information on the protein */

* '''Description:''' succinyl-CoA synthetase (alpha subunit) <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sucD''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || succinyl-CoA synthetase (alpha subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 31 kDa, 5.587
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 900 bp, 300 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sucC]], [[smf]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13483]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:sucD_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16100

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sucCD.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12681]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + succinate + CoA = ADP + phosphate + succinyl-CoA (according to Swiss-Prot)

* '''Protein family:''' succinate/malate CoA ligase alpha subunit family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]

* '''Domains:'''

* '''Modification:''' phosphorylation on (Ser-19 OR Thr-20) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by 2-oxoglutarate, ATP and NADH [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]
*** GTP is not accept by the enzyme [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1JKJ 1JKJ] (E. coli)

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P80865 P80865]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16100]

* '''E.C. number:''' [http://www.expasy.org/enzyme/6.2.1.5 6.2.1.5]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[sucC]]''-''[[SucD]]''

* '''Sigma factor:'''

* '''Regulation:''' repressed by glucose (2.4-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]

* '''Regulatory mechanism:''' [[CcpA]]: transcription repression

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP720 (spc), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>12850135 17218307, </pubmed>
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

CitZ

2009-06-10T15:47:16Z

Cadu Cunha: /* Extended information on the protein */

* '''Description:''' citrate synthase <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citZ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citA2 ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || citrate synthase II
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 5.451
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1116 bp, 372 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytwI]], [[icd]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14874]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:citZ_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29140

===Phenotypes of a mutant ===
glutamate auxotrophy and a defect in sporulation [http://www.ncbi.nlm.nih.gov/pubmed/8045898 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10855]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Acetyl-CoA + H<sub>2</sub>O + oxaloacetate = citrate + CoA (according to Swiss-Prot)

* '''Protein family:''' citrate synthase family (according to Swiss-Prot)

* '''Paralogous protein(s):''' [[MmgD]], [[CitA]]

=== Extended information on the protein ===

* '''Kinetic information:''' Michaelis-Menten (Random Sequential Reaction Mechanism) [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-284 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by acetyl-CoA, 2-oxoglutarate and NADH [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-44C8RWC-SH&_user=5731894&_coverDate=01%2F01%2F1985&_rdoc=28&_fmt=high&_orig=browse&_srch=doc-info(%23toc%234938%231985%23998209998%23270526%23FLP%23display%23Volume)&_cdi=4938&_sort=d&_docanchor=&_ct=40&_acct=C000043105&_version=1&_urlVersion=0&_userid=5731894&md5=f14f4734123ab1177d7217cab6c7ce7d FEBS Letters]
** Inhibited by citrate and CoA (competitively against acetyl-CoA and non-competitively against oxaloacetate) [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
** Inhibited by ATP competitively in ''B. subtilis'' strain 168 and HS 1A17 [http://www.ncbi.nlm.nih.gov/sites/entrez/4980242 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
*** In ''B. subtilis'' strain HS 2A2, ATP inhibits a non-competitive fashion [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
** Activated by AMP [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2C6X 2C6X]

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39120 P39120]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29140]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.3.3.1 2.3.3.1]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[citZ]]-[[icd]]-[[mdh]]''

* '''Sigma factor:''' [[SigA]]

* '''Regulation:''' repressed by glucose (6.7-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed], catabolite repression ([[CcpA]]), repression by glucose + glutamate ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed], repression under anaerobic conditions [http://www.ncbi.nlm.nih.gov/pubmed/9642180 PubMed]

* '''Regulatory mechanism:''' [[CcpA]]: transcription repression, [[CcpA]]: transcription repression, [[CcpC]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP678 (erm), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1120 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:''' available in [[Linc Sonenshein]] lab

=Labs working on this gene/protein=

[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

[[Stülke|Jörg Stülke]], University of Göttingen, Germany
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]

=Your additional remarks=

=References=

<pubmed>12850135 17218307 12100558 9642180 8045898 8655569 4211224 </pubmed>
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
# Kim HJ, Roux A, Sonenshein AL (2002b) Direct and indirect roles of CcpA in regulation of ''Bacillus subtilis'' Krebs cycle genes. Mol Microbiol 45:179-190. [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]
# Nakano MM, Zuber P, Sonenshein AL (1998) Anaerobic regulation of ''Bacillus subtilis'' Krebs cycle genes. ''J Bacteriol.'' '''180:''' 3304-3311. [http://www.ncbi.nlm.nih.gov/pubmed/9642180 PubMed]
# Jin S, Sonenshein AL (1994) Identification of two distinct ''Bacillus subtilis'' citrate synthase genes ''J Bacteriol.'' '''176:''' 4669-4679. [http://www.ncbi.nlm.nih.gov/pubmed/8045898 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Icd

2009-06-10T15:22:57Z

Cadu Cunha: /* Extended information on the protein */

* '''Description:''' isocitrate dehydrogenase <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''icd''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citC ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || isocitrate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46 kDa, 4.833
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1269 bp, 423 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[citZ]], [[mdh]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14873]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:icd_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29130

===Phenotypes of a mutant ===
reduced ability to sporulate [http://www.ncbi.nlm.nih.gov/pubmed/9244258 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10856]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Isocitrate + NADP<sup>+</sup> = 2-oxoglutarate + CO<sub>2</sub> + NADPH (according to Swiss-Prot)

* '''Protein family:''' isocitrate and isopropylmalate dehydrogenases family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/4147570 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylated [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]

* '''Cofactor(s):''' Mg2+, Mn2+

* '''Effectors of protein activity:'''
** Inhibited by glyoxylate, oxaloacetate and oxalomalate [http://www.ncbi.nlm.nih.gov/pubmed/4147570 PubMed]
*** Better inhibition when glyoxylate and oxaloacetate is combined, probably due to the non-enzymatic conversion into oxalomalate, which is a strong inhibitor [http://www.ncbi.nlm.nih.gov/pubmed/4147570 PubMed]

* '''Interactions:'''

* '''Localization:''' attached to the membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1HQS 1HQS]

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39126 P39126]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29130]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.42 1.1.1.42]

=== Additional information===
This enzyme requires NADP+ exclusively. No activity was seen on the presence on NAD+ [http://www.ncbi.nlm.nih.gov/pubmed/4147570 PubMed]

=Expression and regulation=

* '''Operon:'''
**''[[citZ]]-[[icd]]-[[mdh]]''
**''[[icd]]-[[mdh]]''

* '''Sigma factor:''' [[SigA]]

* '''Regulation:''' repressed by glucose (2.2-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed], ''[[citZ]]'': catabolite repression ([[CcpA]]), repression by glucose + glutamate ([[CcpC]])
''[[icd]]'': constitutive
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP666 (spc), GP672 (erm), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1121 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:''' available in [[Linc Sonenshein]] lab

=Labs working on this gene/protein=

[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

=Your additional remarks=

=References=

<pubmed>12850135 10348849 11751849 18763711 17726680 16493705, </pubmed>
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
# Matsuno K, Blais T, Serio AW, Conway T, Henkin TM, Sonenshein AL (1999) Metabolic imbalance and sporulation in an isocitrate dehydrogenase mutant of Bacillus subtilis. J Bacteriol 181:3382-3391. [http://www.ncbi.nlm.nih.gov/sites/entrez/10348849 PubMed]
# Singh SK, Miller SP, Dean A, Banaszak LJ, LaPorte DC (2002) Bacillus subtilis isocitrate dehydrogenase. A substrate analogue for Escherichia coli isocitrate dehydrogenase kinase/ phosphatase. J Biol Chem 277: 7567-7573. [http://www.ncbi.nlm.nih.gov/sites/entrez/11751849 PubMed]
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics 8: 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
# Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in ''Bacillus subtilis''. Proteomics 7: 3509-3526. [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
# Levine et al. (2006) Analysis of the dynamic ''Bacillus subtilis'' Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. Proteomics 6, 2157-2173. [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Icd

2009-06-10T15:22:30Z

Cadu Cunha: /* Database entries */

* '''Description:''' isocitrate dehydrogenase <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''icd''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citC ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || isocitrate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46 kDa, 4.833
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1269 bp, 423 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[citZ]], [[mdh]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14873]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:icd_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29130

===Phenotypes of a mutant ===
reduced ability to sporulate [http://www.ncbi.nlm.nih.gov/pubmed/9244258 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10856]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Isocitrate + NADP<sup>+</sup> = 2-oxoglutarate + CO<sub>2</sub> + NADPH (according to Swiss-Prot)

* '''Protein family:''' isocitrate and isopropylmalate dehydrogenases family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/4147570 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylated [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by glyoxylate, oxaloacetate and oxalomalate [http://www.ncbi.nlm.nih.gov/pubmed/4147570 PubMed]
*** Better inhibition when glyoxylate and oxaloacetate is combined, probably due to the non-enzymatic conversion into oxalomalate, which is a strong inhibitor [http://www.ncbi.nlm.nih.gov/pubmed/4147570 PubMed]

* '''Interactions:'''

* '''Localization:''' attached to the membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1HQS 1HQS]

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39126 P39126]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29130]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.42 1.1.1.42]

=== Additional information===
This enzyme requires NADP+ exclusively. No activity was seen on the presence on NAD+ [http://www.ncbi.nlm.nih.gov/pubmed/4147570 PubMed]

=Expression and regulation=

* '''Operon:'''
**''[[citZ]]-[[icd]]-[[mdh]]''
**''[[icd]]-[[mdh]]''

* '''Sigma factor:''' [[SigA]]

* '''Regulation:''' repressed by glucose (2.2-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed], ''[[citZ]]'': catabolite repression ([[CcpA]]), repression by glucose + glutamate ([[CcpC]])
''[[icd]]'': constitutive
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP666 (spc), GP672 (erm), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1121 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:''' available in [[Linc Sonenshein]] lab

=Labs working on this gene/protein=

[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

=Your additional remarks=

=References=

<pubmed>12850135 10348849 11751849 18763711 17726680 16493705, </pubmed>
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
# Matsuno K, Blais T, Serio AW, Conway T, Henkin TM, Sonenshein AL (1999) Metabolic imbalance and sporulation in an isocitrate dehydrogenase mutant of Bacillus subtilis. J Bacteriol 181:3382-3391. [http://www.ncbi.nlm.nih.gov/sites/entrez/10348849 PubMed]
# Singh SK, Miller SP, Dean A, Banaszak LJ, LaPorte DC (2002) Bacillus subtilis isocitrate dehydrogenase. A substrate analogue for Escherichia coli isocitrate dehydrogenase kinase/ phosphatase. J Biol Chem 277: 7567-7573. [http://www.ncbi.nlm.nih.gov/sites/entrez/11751849 PubMed]
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics 8: 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
# Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in ''Bacillus subtilis''. Proteomics 7: 3509-3526. [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
# Levine et al. (2006) Analysis of the dynamic ''Bacillus subtilis'' Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. Proteomics 6, 2157-2173. [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Icd

2009-06-10T15:22:15Z

Cadu Cunha: /* Additional information */

* '''Description:''' isocitrate dehydrogenase <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''icd''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citC ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || isocitrate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46 kDa, 4.833
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1269 bp, 423 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[citZ]], [[mdh]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14873]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:icd_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29130

===Phenotypes of a mutant ===
reduced ability to sporulate [http://www.ncbi.nlm.nih.gov/pubmed/9244258 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10856]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Isocitrate + NADP<sup>+</sup> = 2-oxoglutarate + CO<sub>2</sub> + NADPH (according to Swiss-Prot)

* '''Protein family:''' isocitrate and isopropylmalate dehydrogenases family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/4147570 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylated [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by glyoxylate, oxaloacetate and oxalomalate [http://www.ncbi.nlm.nih.gov/pubmed/4147570 PubMed]
*** Better inhibition when glyoxylate and oxaloacetate is combined, probably due to the non-enzymatic conversion into oxalomalate, which is a strong inhibitor [http://www.ncbi.nlm.nih.gov/pubmed/4147570 PubMed]

* '''Interactions:'''

* '''Localization:''' attached to the membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1HQS 1HQS]

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39126 P39126]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29130]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.42 1.1.1.42] 2

=== Additional information===
This enzyme requires NADP+ exclusively. No activity was seen on the presence on NAD+ [http://www.ncbi.nlm.nih.gov/pubmed/4147570 PubMed]

=Expression and regulation=

* '''Operon:'''
**''[[citZ]]-[[icd]]-[[mdh]]''
**''[[icd]]-[[mdh]]''

* '''Sigma factor:''' [[SigA]]

* '''Regulation:''' repressed by glucose (2.2-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed], ''[[citZ]]'': catabolite repression ([[CcpA]]), repression by glucose + glutamate ([[CcpC]])
''[[icd]]'': constitutive
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP666 (spc), GP672 (erm), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1121 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:''' available in [[Linc Sonenshein]] lab

=Labs working on this gene/protein=

[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

=Your additional remarks=

=References=

<pubmed>12850135 10348849 11751849 18763711 17726680 16493705, </pubmed>
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
# Matsuno K, Blais T, Serio AW, Conway T, Henkin TM, Sonenshein AL (1999) Metabolic imbalance and sporulation in an isocitrate dehydrogenase mutant of Bacillus subtilis. J Bacteriol 181:3382-3391. [http://www.ncbi.nlm.nih.gov/sites/entrez/10348849 PubMed]
# Singh SK, Miller SP, Dean A, Banaszak LJ, LaPorte DC (2002) Bacillus subtilis isocitrate dehydrogenase. A substrate analogue for Escherichia coli isocitrate dehydrogenase kinase/ phosphatase. J Biol Chem 277: 7567-7573. [http://www.ncbi.nlm.nih.gov/sites/entrez/11751849 PubMed]
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics 8: 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
# Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in ''Bacillus subtilis''. Proteomics 7: 3509-3526. [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
# Levine et al. (2006) Analysis of the dynamic ''Bacillus subtilis'' Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. Proteomics 6, 2157-2173. [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Icd

2009-06-10T15:21:30Z

Cadu Cunha: /* Extended information on the protein */

* '''Description:''' isocitrate dehydrogenase <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''icd''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citC ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || isocitrate dehydrogenase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46 kDa, 4.833
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1269 bp, 423 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[citZ]], [[mdh]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14873]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:icd_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29130

===Phenotypes of a mutant ===
reduced ability to sporulate [http://www.ncbi.nlm.nih.gov/pubmed/9244258 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10856]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Isocitrate + NADP<sup>+</sup> = 2-oxoglutarate + CO<sub>2</sub> + NADPH (according to Swiss-Prot)

* '''Protein family:''' isocitrate and isopropylmalate dehydrogenases family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/4147570 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylated [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by glyoxylate, oxaloacetate and oxalomalate [http://www.ncbi.nlm.nih.gov/pubmed/4147570 PubMed]
*** Better inhibition when glyoxylate and oxaloacetate is combined, probably due to the non-enzymatic conversion into oxalomalate, which is a strong inhibitor [http://www.ncbi.nlm.nih.gov/pubmed/4147570 PubMed]

* '''Interactions:'''

* '''Localization:''' attached to the membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1HQS 1HQS]

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39126 P39126]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29130]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.42 1.1.1.42] 2

=== Additional information===

=Expression and regulation=

* '''Operon:'''
**''[[citZ]]-[[icd]]-[[mdh]]''
**''[[icd]]-[[mdh]]''

* '''Sigma factor:''' [[SigA]]

* '''Regulation:''' repressed by glucose (2.2-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed], ''[[citZ]]'': catabolite repression ([[CcpA]]), repression by glucose + glutamate ([[CcpC]])
''[[icd]]'': constitutive
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP666 (spc), GP672 (erm), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1121 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:''' available in [[Linc Sonenshein]] lab

=Labs working on this gene/protein=

[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

=Your additional remarks=

=References=

<pubmed>12850135 10348849 11751849 18763711 17726680 16493705, </pubmed>
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
# Matsuno K, Blais T, Serio AW, Conway T, Henkin TM, Sonenshein AL (1999) Metabolic imbalance and sporulation in an isocitrate dehydrogenase mutant of Bacillus subtilis. J Bacteriol 181:3382-3391. [http://www.ncbi.nlm.nih.gov/sites/entrez/10348849 PubMed]
# Singh SK, Miller SP, Dean A, Banaszak LJ, LaPorte DC (2002) Bacillus subtilis isocitrate dehydrogenase. A substrate analogue for Escherichia coli isocitrate dehydrogenase kinase/ phosphatase. J Biol Chem 277: 7567-7573. [http://www.ncbi.nlm.nih.gov/sites/entrez/11751849 PubMed]
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics 8: 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
# Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in ''Bacillus subtilis''. Proteomics 7: 3509-3526. [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
# Levine et al. (2006) Analysis of the dynamic ''Bacillus subtilis'' Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. Proteomics 6, 2157-2173. [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

CitB

2009-06-10T15:16:04Z

Cadu Cunha: /* Basic information/ Evolution */

* '''Description:''' Trigger enzyme: aconitase and RNA binding protein<br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || aconitate hydratase (aconitase)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 99 kDa, 4.903
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2727 bp, 909 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sspO]], [[yneN]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13684]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:citB_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU18000

===Phenotypes of a mutant ===
glutamate auxotrophy and a defect in sporulation [http://www.ncbi.nlm.nih.gov/pubmed/9393699 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citB.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10478]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Citrate = isocitrate (according to Swiss-Prot)
** Binding to iron responsive elements (IRE RNA) in the absence of the FeS cluster [http://www.ncbi.nlm.nih.gov/pubmed/10468622 PubMed]

* '''Protein family:'''

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):''' FeS cluster

* '''Effectors of protein activity:'''

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1L5J 1L5J] (''E. coli'')

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P09339 P09339]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU18000]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.1.3 4.2.1.3]

=== Additional information===
''B. subtilis'' aconitase is both an enzyme and an RNA binding protein [http://www.ncbi.nlm.nih.gov/pubmed/10468622 PubMed]

=Expression and regulation=

* '''Operon:''' ''[[citB]]''

* '''Sigma factor:''' [[SigA]]

* '''Regulation:'''
** repressed by glucose (3.7-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
** repression by glucose + arginine ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/16395550 PubMed]
** less expressed under conditions of extreme iron limitation ([[FsrA]]) [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]

* '''Regulatory mechanism:'''
** [[CcpA]]: transcription repression
** [[CcpC]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]
** [[AbrB]]: transcription activation [http://www.ncbi.nlm.nih.gov/pubmed/12591885 PubMed]
** [[FsrA]]: translational repression [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP683 (erm), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:''' available in [[Linc Sonenshein]] lab

=Labs working on this gene/protein=

[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

[[Stülke|Jörg Stülke]], University of Göttingen, Germany
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]

=Your additional remarks=

=References=

<pubmed>12850135 2413006 10656796 10468622 6143742 12591885 16395550 16923907 9642180 9393699 12591885 2105305, </pubmed>
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
# Rosenkrantz MS, Dingman DW, Sonenshein AL (1985) Bacillus subtilis citB gene is regulated synergistically by glucose and glutamine. J Bacteriol 164:155-164. [http://www.ncbi.nlm.nih.gov/sites/entrez/2413006 PubMed]
# Jourlin-Castelli C, Mani N, Nakano MM, Sonenshein AL (2000) CcpC, a novel regulator of the LysR family required for glucose repression of the citB gene in Bacillus subtilis. J Mol Biol 295:865-878. [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]
# Alén C, Sonenshein AL (1999) Bacillus subtilis aconitase is an RNA-binding protein. Proc Natl Acad Sci USA 96:10412-10417. [http://www.ncbi.nlm.nih.gov/sites/entrez/10468622 PubMed]
# Fisher SH, Magasanik B (1984) 2-Ketoglutarate and the regulation of aconitase and histidase formation Bacillus subtilis. J Bacteriol 158:379-382. [http://www.ncbi.nlm.nih.gov/sites/entrez/6143742 PubMed]
# Kim, H. J., S. I. Kim, M. Ratnayake-Lecamwasam, K. Tachikawa, A. L. Sonenshein, and M. Strauch. (2003) Complex regulation of the Bacillus subtilis aconitase gene. J. Bacteriol. 185:1672-1680. [http://www.ncbi.nlm.nih.gov/sites/entrez/12591885 PubMed]
# Blencke, H.-M., Reif, I., Commichau, F. M., Detsch, C., Wacker, I., Ludwig, H. & Stülke, J. (2006) Regulation of citB expression in Bacillus subtilis: Integration of multiple metabolic signals in the citrate pool and by the general nitrogen regulatory system. Arch. Microbiol. 185: 136-146. [http://www.ncbi.nlm.nih.gov/sites/entrez/16395550 PubMed]
# Serio, A. W., Pechter, K. B., and Sonenshein, A. L. (2006) Bacillus subtilis aconitase is required for efficient late-sporulation gene expression. J Bacteriol 188: 6396-6405. [http://www.ncbi.nlm.nih.gov/sites/entrez/16923907 PubMed]
# Nakano MM, Zuber P, Sonenshein AL (1998) Anaerobic regulation of ''Bacillus subtilis'' Krebs cycle genes. J Bacteriol. 180:3304-3311. [http://www.ncbi.nlm.nih.gov/pubmed/9642180 PubMed]
# Craig JE, Ford MJ, Blaydon DC, Sonenshein AL (1997) A null mutation in the ''Bacillus subtilis'' aconitase gene causes a block in Spo0A-phosphate-dependent gene expression. J Bacteriol 197:7351-7359. [http://www.ncbi.nlm.nih.gov/pubmed/9393699 PubMed]
# Kim HJ, Kim SI, Ratnayake-Lecamwasam M, Tachikawa K, Sonenshein AL, Strauch M (2003) Complex regulation of the ''Bacillus subtilis'' aconitase gene. J Bacteriol. 185:1672-1680. [http://www.ncbi.nlm.nih.gov/pubmed/12591885 PubMed]
# Fouet, A., and Sonenshein, A. L. (1990) A target for carbon source-dependent negative regulation of the ''citB'' promoter of ''Bacillus subtilis''. J Bacteriol 172: 835-844. [http://www.ncbi.nlm.nih.gov/sites/entrez/2105305 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

CitZ

2009-06-10T15:09:18Z

Cadu Cunha: /* References */

* '''Description:''' citrate synthase <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citZ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citA2 ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || citrate synthase II
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 5.451
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1116 bp, 372 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytwI]], [[icd]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14874]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:citZ_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29140

===Phenotypes of a mutant ===
glutamate auxotrophy and a defect in sporulation [http://www.ncbi.nlm.nih.gov/pubmed/8045898 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10855]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Acetyl-CoA + H<sub>2</sub>O + oxaloacetate = citrate + CoA (according to Swiss-Prot)

* '''Protein family:''' citrate synthase family (according to Swiss-Prot)

* '''Paralogous protein(s):''' [[MmgD]], [[CitA]]

=== Extended information on the protein ===

* '''Kinetic information:''' Michaelis-Menten (Random Sequential Reaction Mechanism) [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-284 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by acetyl-CoA [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
** Inhibited by citrate and CoA (competitively against acetyl-CoA and non-competitively against oxaloacetate) [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
** Inhibited by ATP competitively in ''B. subtilis'' strain 168 and HS 1A17 [http://www.ncbi.nlm.nih.gov/sites/entrez/4980242 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
*** In ''B. subtilis'' strain HS 2A2, ATP inhibits a non-competitive fashion [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
** Activated by AMP [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2C6X 2C6X]

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39120 P39120]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29140]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.3.3.1 2.3.3.1]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[citZ]]-[[icd]]-[[mdh]]''

* '''Sigma factor:''' [[SigA]]

* '''Regulation:''' repressed by glucose (6.7-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed], catabolite repression ([[CcpA]]), repression by glucose + glutamate ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed], repression under anaerobic conditions [http://www.ncbi.nlm.nih.gov/pubmed/9642180 PubMed]

* '''Regulatory mechanism:''' [[CcpA]]: transcription repression, [[CcpA]]: transcription repression, [[CcpC]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP678 (erm), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1120 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:''' available in [[Linc Sonenshein]] lab

=Labs working on this gene/protein=

[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

[[Stülke|Jörg Stülke]], University of Göttingen, Germany
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]

=Your additional remarks=

=References=

<pubmed>12850135 17218307 12100558 9642180 8045898 8655569 4211224 </pubmed>
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
# Kim HJ, Roux A, Sonenshein AL (2002b) Direct and indirect roles of CcpA in regulation of ''Bacillus subtilis'' Krebs cycle genes. Mol Microbiol 45:179-190. [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]
# Nakano MM, Zuber P, Sonenshein AL (1998) Anaerobic regulation of ''Bacillus subtilis'' Krebs cycle genes. ''J Bacteriol.'' '''180:''' 3304-3311. [http://www.ncbi.nlm.nih.gov/pubmed/9642180 PubMed]
# Jin S, Sonenshein AL (1994) Identification of two distinct ''Bacillus subtilis'' citrate synthase genes ''J Bacteriol.'' '''176:''' 4669-4679. [http://www.ncbi.nlm.nih.gov/pubmed/8045898 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

CitZ

2009-06-10T15:08:22Z

Cadu Cunha: /* Extended information on the protein */

* '''Description:''' citrate synthase <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citZ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citA2 ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || citrate synthase II
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 5.451
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1116 bp, 372 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytwI]], [[icd]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14874]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:citZ_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29140

===Phenotypes of a mutant ===
glutamate auxotrophy and a defect in sporulation [http://www.ncbi.nlm.nih.gov/pubmed/8045898 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10855]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Acetyl-CoA + H<sub>2</sub>O + oxaloacetate = citrate + CoA (according to Swiss-Prot)

* '''Protein family:''' citrate synthase family (according to Swiss-Prot)

* '''Paralogous protein(s):''' [[MmgD]], [[CitA]]

=== Extended information on the protein ===

* '''Kinetic information:''' Michaelis-Menten (Random Sequential Reaction Mechanism) [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-284 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by acetyl-CoA [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
** Inhibited by citrate and CoA (competitively against acetyl-CoA and non-competitively against oxaloacetate) [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
** Inhibited by ATP competitively in ''B. subtilis'' strain 168 and HS 1A17 [http://www.ncbi.nlm.nih.gov/sites/entrez/4980242 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
*** In ''B. subtilis'' strain HS 2A2, ATP inhibits a non-competitive fashion [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
** Activated by AMP [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2C6X 2C6X]

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39120 P39120]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29140]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.3.3.1 2.3.3.1]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[citZ]]-[[icd]]-[[mdh]]''

* '''Sigma factor:''' [[SigA]]

* '''Regulation:''' repressed by glucose (6.7-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed], catabolite repression ([[CcpA]]), repression by glucose + glutamate ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed], repression under anaerobic conditions [http://www.ncbi.nlm.nih.gov/pubmed/9642180 PubMed]

* '''Regulatory mechanism:''' [[CcpA]]: transcription repression, [[CcpA]]: transcription repression, [[CcpC]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP678 (erm), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1120 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:''' available in [[Linc Sonenshein]] lab

=Labs working on this gene/protein=

[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

[[Stülke|Jörg Stülke]], University of Göttingen, Germany
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]

=Your additional remarks=

=References=

<pubmed>12850135 17218307 12100558 9642180 8045898, </pubmed>
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
# Kim HJ, Roux A, Sonenshein AL (2002b) Direct and indirect roles of CcpA in regulation of ''Bacillus subtilis'' Krebs cycle genes. Mol Microbiol 45:179-190. [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]
# Nakano MM, Zuber P, Sonenshein AL (1998) Anaerobic regulation of ''Bacillus subtilis'' Krebs cycle genes. ''J Bacteriol.'' '''180:''' 3304-3311. [http://www.ncbi.nlm.nih.gov/pubmed/9642180 PubMed]
# Jin S, Sonenshein AL (1994) Identification of two distinct ''Bacillus subtilis'' citrate synthase genes ''J Bacteriol.'' '''176:''' 4669-4679. [http://www.ncbi.nlm.nih.gov/pubmed/8045898 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

CitZ

2009-06-10T15:07:58Z

Cadu Cunha: /* Extended information on the protein */

* '''Description:''' citrate synthase <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citZ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citA2 ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || citrate synthase II
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 5.451
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1116 bp, 372 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytwI]], [[icd]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14874]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:citZ_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29140

===Phenotypes of a mutant ===
glutamate auxotrophy and a defect in sporulation [http://www.ncbi.nlm.nih.gov/pubmed/8045898 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10855]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Acetyl-CoA + H<sub>2</sub>O + oxaloacetate = citrate + CoA (according to Swiss-Prot)

* '''Protein family:''' citrate synthase family (according to Swiss-Prot)

* '''Paralogous protein(s):''' [[MmgD]], [[CitA]]

=== Extended information on the protein ===

* '''Kinetic information:''' Michaelis-Menten (Random Sequential Reaction Mechanism) [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-284 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by acetyl-CoA [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
** Inhibited by citrate and CoA (competitively against acetyl-CoA and non-competitively against oxaloacetate) [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
** Inhibited by ATP competitively in ''B. subtilis'' strain 168 and HS 1A17 [http://www.ncbi.nlm.nih.gov/sites/entrez/4980242 PubMed] [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
*** In ''B. subtilis'' strain HS 2A2, ATP inhibits in a non-competitive fashion [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
** Activated by AMP [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2C6X 2C6X]

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39120 P39120]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29140]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.3.3.1 2.3.3.1]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[citZ]]-[[icd]]-[[mdh]]''

* '''Sigma factor:''' [[SigA]]

* '''Regulation:''' repressed by glucose (6.7-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed], catabolite repression ([[CcpA]]), repression by glucose + glutamate ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed], repression under anaerobic conditions [http://www.ncbi.nlm.nih.gov/pubmed/9642180 PubMed]

* '''Regulatory mechanism:''' [[CcpA]]: transcription repression, [[CcpA]]: transcription repression, [[CcpC]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP678 (erm), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1120 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:''' available in [[Linc Sonenshein]] lab

=Labs working on this gene/protein=

[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

[[Stülke|Jörg Stülke]], University of Göttingen, Germany
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]

=Your additional remarks=

=References=

<pubmed>12850135 17218307 12100558 9642180 8045898, </pubmed>
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
# Kim HJ, Roux A, Sonenshein AL (2002b) Direct and indirect roles of CcpA in regulation of ''Bacillus subtilis'' Krebs cycle genes. Mol Microbiol 45:179-190. [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]
# Nakano MM, Zuber P, Sonenshein AL (1998) Anaerobic regulation of ''Bacillus subtilis'' Krebs cycle genes. ''J Bacteriol.'' '''180:''' 3304-3311. [http://www.ncbi.nlm.nih.gov/pubmed/9642180 PubMed]
# Jin S, Sonenshein AL (1994) Identification of two distinct ''Bacillus subtilis'' citrate synthase genes ''J Bacteriol.'' '''176:''' 4669-4679. [http://www.ncbi.nlm.nih.gov/pubmed/8045898 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

CitZ

2009-06-10T15:02:43Z

Cadu Cunha: /* Extended information on the protein */

* '''Description:''' citrate synthase <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citZ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citA2 ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || citrate synthase II
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 5.451
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1116 bp, 372 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytwI]], [[icd]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14874]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:citZ_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29140

===Phenotypes of a mutant ===
glutamate auxotrophy and a defect in sporulation [http://www.ncbi.nlm.nih.gov/pubmed/8045898 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10855]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Acetyl-CoA + H<sub>2</sub>O + oxaloacetate = citrate + CoA (according to Swiss-Prot)

* '''Protein family:''' citrate synthase family (according to Swiss-Prot)

* '''Paralogous protein(s):''' [[MmgD]], [[CitA]]

=== Extended information on the protein ===

* '''Kinetic information:''' Michaelis-Menten [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-284 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited by acetyl-CoA [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
** Inhibited by citrate and CoA (competitively against acetyl-CoA and non-competitively against oxaloacetate) [http://www.ncbi.nlm.nih.gov/sites/entrez/4211224 PubMed]
** Inhibited by ATP [http://www.ncbi.nlm.nih.gov/sites/entrez/4980242 PubMed]

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2C6X 2C6X]

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39120 P39120]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29140]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.3.3.1 2.3.3.1]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[citZ]]-[[icd]]-[[mdh]]''

* '''Sigma factor:''' [[SigA]]

* '''Regulation:''' repressed by glucose (6.7-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed], catabolite repression ([[CcpA]]), repression by glucose + glutamate ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed], repression under anaerobic conditions [http://www.ncbi.nlm.nih.gov/pubmed/9642180 PubMed]

* '''Regulatory mechanism:''' [[CcpA]]: transcription repression, [[CcpA]]: transcription repression, [[CcpC]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP678 (erm), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1120 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:''' available in [[Linc Sonenshein]] lab

=Labs working on this gene/protein=

[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

[[Stülke|Jörg Stülke]], University of Göttingen, Germany
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]

=Your additional remarks=

=References=

<pubmed>12850135 17218307 12100558 9642180 8045898, </pubmed>
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
# Kim HJ, Roux A, Sonenshein AL (2002b) Direct and indirect roles of CcpA in regulation of ''Bacillus subtilis'' Krebs cycle genes. Mol Microbiol 45:179-190. [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]
# Nakano MM, Zuber P, Sonenshein AL (1998) Anaerobic regulation of ''Bacillus subtilis'' Krebs cycle genes. ''J Bacteriol.'' '''180:''' 3304-3311. [http://www.ncbi.nlm.nih.gov/pubmed/9642180 PubMed]
# Jin S, Sonenshein AL (1994) Identification of two distinct ''Bacillus subtilis'' citrate synthase genes ''J Bacteriol.'' '''176:''' 4669-4679. [http://www.ncbi.nlm.nih.gov/pubmed/8045898 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

CitZ

2009-06-10T14:49:52Z

Cadu Cunha: /* Basic information/ Evolution */

* '''Description:''' citrate synthase <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''citZ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citA2 ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || citrate synthase II
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 5.451
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1116 bp, 372 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytwI]], [[icd]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14874]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:citZ_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU29140

===Phenotypes of a mutant ===
glutamate auxotrophy and a defect in sporulation [http://www.ncbi.nlm.nih.gov/pubmed/8045898 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10855]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Acetyl-CoA + H<sub>2</sub>O + oxaloacetate = citrate + CoA (according to Swiss-Prot)

* '''Protein family:''' citrate synthase family (according to Swiss-Prot)

* '''Paralogous protein(s):''' [[MmgD]], [[CitA]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' phosphorylation on Ser-284 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:''' inhibited by ATP [http://www.ncbi.nlm.nih.gov/sites/entrez/4980242 PubMed]

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2C6X 2C6X]

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39120 P39120]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29140]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.3.3.1 2.3.3.1]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[citZ]]-[[icd]]-[[mdh]]''

* '''Sigma factor:''' [[SigA]]

* '''Regulation:''' repressed by glucose (6.7-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed], catabolite repression ([[CcpA]]), repression by glucose + glutamate ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed], repression under anaerobic conditions [http://www.ncbi.nlm.nih.gov/pubmed/9642180 PubMed]

* '''Regulatory mechanism:''' [[CcpA]]: transcription repression, [[CcpA]]: transcription repression, [[CcpC]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP678 (erm), available in [[Stülke]] lab

* '''Expression vector:'''
** pGP1120 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Stülke]] lab)
* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:''' available in [[Linc Sonenshein]] lab

=Labs working on this gene/protein=

[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]

[[Stülke|Jörg Stülke]], University of Göttingen, Germany
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]

=Your additional remarks=

=References=

<pubmed>12850135 17218307 12100558 9642180 8045898, </pubmed>
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
# Kim HJ, Roux A, Sonenshein AL (2002b) Direct and indirect roles of CcpA in regulation of ''Bacillus subtilis'' Krebs cycle genes. Mol Microbiol 45:179-190. [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed]
# Nakano MM, Zuber P, Sonenshein AL (1998) Anaerobic regulation of ''Bacillus subtilis'' Krebs cycle genes. ''J Bacteriol.'' '''180:''' 3304-3311. [http://www.ncbi.nlm.nih.gov/pubmed/9642180 PubMed]
# Jin S, Sonenshein AL (1994) Identification of two distinct ''Bacillus subtilis'' citrate synthase genes ''J Bacteriol.'' '''176:''' 4669-4679. [http://www.ncbi.nlm.nih.gov/pubmed/8045898 PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

PdhD

2009-06-10T14:48:17Z

Cadu Cunha: /* References */

* '''Description:''' dihydrolipoamide dehydrogenase E3 subunit of both pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase complexes <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pdhD''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citL ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || dihydrolipoamide dehydrogenase E3 subunit<br/> of both pyruvate dehydrogenase and 2-oxoglutarate<br/> dehydrogenase complexes
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || links glycolysis and TCA cycle, enzyme in TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 49 kDa, 4.76
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1410 bp, 470 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pdhC]]'', ''[[slp]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13334]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:pdhD_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/><br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU14610

===Phenotypes of a mutant ===

* defects in sporulation and unable to grow on glucose as single carbon source [http://www.ncbi.nlm.nih.gov/pubmed/11976308 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pdhABCD.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10210]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Protein N(6)-(dihydrolipoyl)lysine + NAD<sup>+</sup> = protein N(6)-(lipoyl)lysine + NADH (according to Swiss-Prot)

* '''Protein family:''' class-I pyridine nucleotide-disulfide oxidoreductase family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/6414463 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylated (Ser/Thr/Tyr) [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited thiamine 2-thiothiazolone diphosphate and NADH [http://www.ncbi.nlm.nih.gov/pubmed/6414463 PubMed]
** Low sensibility to NADPH

* '''Interactions:''' [[OdhA]]-[[OdhB]]-[[PdhD]], [[PdhA]]-[[PdhB]]-[[PdhC]]-[[PdhD]]

* '''Localization:''' cytoplasm (according to Swiss-Prot)

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1EBD 1EBD] (complex with binding domain of dihydrolipoamide acetylase, Geobacillus stearothermophilus), [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1EBD 1EBD] (complex with binding domain of dihydrolipoamide acetylase, ''Geobacillus stearothermophilus'')

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P21880 P21880]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14610]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.8.1.4 1.8.1.4]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[pdhA]]-[[pdhB]]-[[pdhC]]-[[pdhD]]''

* '''Sigma factor:''' [[SigA]]

* '''Regulation:''' expression activated by glucose (2.0 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>12850135 6414463 </pubmed>
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
# Gao et al. (2002) The E1beta and E2 subunits of the ''Bacillus subtilis'' pyruvate dehydrogenase complex are involved in regulation of sporulation.''J. Bacteriol.'' '''184:''' 2780-2788. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

PdhC

2009-06-10T14:48:08Z

Cadu Cunha: /* References */

* '''Description:''' pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit) <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pdhC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || pyruvate dehydrogenase <br/>(dihydrolipoamide acetyltransferase E2 subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || links glycolysis and TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 4.855
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1326 bp, 442 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pdhB]]'', ''[[pdhD]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13333]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:pdhC_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU14600

===Phenotypes of a mutant ===

* defects in sporulation and unable to grow on glucose as single carbon source [http://www.ncbi.nlm.nih.gov/pubmed/11976308 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pdhABCD.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10209]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Acetyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-acetyldihydrolipoyl)lysine (according to Swiss-Prot)

* '''Protein family:''' lipoyl-binding domain (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/6414463 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylated (Ser/Thr/Tyr) [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited thiamine 2-thiothiazolone diphosphate and NADH [http://www.ncbi.nlm.nih.gov/pubmed/6414463 PubMed]
** Low sensibility to NADPH

* '''Interactions:''' [[PdhA]]-[[PdhB]]-[[PdhC]]-[[PdhD]]

* '''Localization:''' membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1W88 1W88] (E1 in complex with subunit binding domain of E2, ''Geobacillus stearothermophilus''), [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2PDE 2PDE] (peripheral subunit binding domain, ''Geobacillus stearothermophilus''), [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1LAC 1LAC] (lipoyl domain, ''Geobacillus stearothermophilus''), [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1B5S 1B5S] (catalytic domain (residues 184-425) , ''Geobacillus stearothermophilus'')
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P21883 P21883]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14600]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.3.1.12 2.3.1.12] 2

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[pdhA]]-[[pdhB]]-[[pdhC]]-[[pdhD]]''

* '''Sigma factor:''' [[SigA]]

* '''Regulation:''' expression activated by glucose (1.9 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

[[Arthur Aronson]], Purdue University, West Lafayette, USA [http://wwwdev.gradschool.purdue.edu/PULSe/faculty.cfm?fid=5&range=0 homepage]

=Your additional remarks=

=References=

<pubmed>12850135 18763711 6414463 </pubmed>
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics 8: 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
# Gao et al. (2002) The E1beta and E2 subunits of the ''Bacillus subtilis'' pyruvate dehydrogenase complex are involved in regulation of sporulation.''J. Bacteriol.'' '''184:''' 2780-2788. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

PdhB

2009-06-10T14:47:58Z

Cadu Cunha: /* References */

* '''Description:''' pyruvate dehydrogenase (E1 beta subunit) <br/><br/>

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''pdhB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || pyruvate dehydrogenase (E1 beta subunit)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || links glycolysis and TCA cycle
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 35 kDa, 4.547
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 975 bp, 325 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pdhA]]'', ''[[pdhC]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13332]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:pdhB_context.gif]]
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
|-
|}

__TOC__

<br/><br/>

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU14590

===Phenotypes of a mutant ===
* defects in sporulation and unable to grow on glucose as single carbon source [http://www.ncbi.nlm.nih.gov/pubmed/11976308 PubMed]

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pdhABCD.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10208]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' Pyruvate + [dihydrolipoyllysine-residue acetyltransferase] lipoyllysine = [dihydrolipoyllysine-residue acetyltransferase] S-acetyldihydrolipoyllysine + CO<sub>2</sub> (according to Swiss-Prot)

* '''Protein family:'''

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:''' Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/6414463 PubMed]

* '''Domains:'''

* '''Modification:''' phosphorylation on (Ser-302 OR Ser-306) [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** Inhibited thiamine 2-thiothiazolone diphosphate and NADH [http://www.ncbi.nlm.nih.gov/pubmed/6414463 PubMed]
** Low sensibility to NADPH

* '''Interactions:''' [[PdhA]]-[[PdhB]]-[[PdhC]]-[[PdhD]]

* '''Localization:''' membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1W88 1W88] (E1 in complex with subunit binding domain of E2, ''Geobacillus stearothermophilus'')

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P21882 P21882]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14590]

* '''E.C. number:''' [http://www.expasy.org/enzyme/1.2.4.1 1.2.4.1]

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[pdhA]]-[[pdhB]]-[[pdhC]]-[[pdhD]]''

* '''Sigma factor:''' [[SigA]]

* '''Regulation:''' expression activated by glucose (2.8 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' GP459 (spc), available in [[Stülke]] lab

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

[[Arthur Aronson]], Purdue University, West Lafayette, USA [http://wwwdev.gradschool.purdue.edu/PULSe/faculty.cfm?fid=5&range=0 homepage]

=Your additional remarks=

=References=

<pubmed>12850135 17218307 18763711 6414463 </pubmed>
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics 8: 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
# Gao et al. (2002) The E1beta and E2 subunits of the ''Bacillus subtilis'' pyruvate dehydrogenase complex are involved in regulation of sporulation.''J. Bacteriol.'' '''184:''' 2780-2788. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]