Difference between revisions of "Sandbox"

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−
* '''Description:''' Carbon catabolite control protein A, involved in glucose regulation of many genes; represses catabolic genes and activates genes involved in excretion of excess carbon <br/><br/>
+
* '''Description:''' glutamine-fructose-6-phosphate transaminase <br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Gene name'''
+
|style="background:#ABCDEF;" align="center"|'''Gene name''' glaube ich oder nicht
−
|''ccpA''
+
|''glmS''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''graR, alsA, amyR''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''gcaA, ybxD ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator
+
|style="background:#ABCDEF;" align="center"| '''Product''' || glutamine-fructose-6-phosphate transaminase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || mediates carbon catabolite repression (CCR)
+
|style="background:#ABCDEF;" align="center"|'''Function''' || cell wall synthesis
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/nucleosides_catabolism.html Nucleoside catabolism], [http://subtiwiki.uni-goettingen.de/pathways/gene_regulation_nucleotides.html Nucleotides (regulation)], [http://subtiwiki.uni-goettingen.de/pathways/ile_val_leu.html Ile, Leu, Val],<br/>[http://subtiwiki.uni-goettingen.de/pathways/histidine.html His], [http://subtiwiki.uni-goettingen.de/pathways/CoA_synthesis.html Coenzyme A], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
+
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=sandbox sandbox]'''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 36,8 kDa, 5.06
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 65 kDa, 4.796 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1002 bp, 334 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1800 bp, 600 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[aroA]]'', ''[[motP]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[glmM]]'', ''[[ybbU]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14952&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11954&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ccpA_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:quintos.gif]]
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 +
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:test.gif]]
 +
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 +
|-
 +
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=glmS_200277_202079_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:glmS_expression.png|500px]]
 
|-
 
|-
 
|}
 
|}
  
 
__TOC__
 
__TOC__
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
 +
<br/><br/><br/><br/>
  
−
<br/><br/><br/><br/><br/><br/>
 
  
 +
<br/><br/>
 +
 +
= [[Categories]] containing this gene/protein =
 +
{{SubtiWiki category|[[cell wall synthesis]]}},
 +
{{SubtiWiki category|[[biosynthesis of cell wall components]]}},
 +
{{SubtiWiki category|[[essential genes]]}}
 +
 +
= This gene is a member of the following [[regulons]] =
 +
{{SubtiWiki regulon|[[glmS ribozyme]]}}
  
 
=The gene=
 
=The gene=
Line 38: Line 57:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU29740
+
* '''Locus tag:''' BSU01780
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
  
−
Loss of carbon catabolite repression.  
+
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
−
Loss of PTS-dependent sugar transport due to excessive phosphorylation of [[PtsH |HPr]] by [[HprK]].
 
−
The mutant is unable to grow on a minimal medium with glucose and ammonium as the only sources of carbon and nitrogen, respectively.
 
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [HELLO BSU00100]
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00240&redirect=T"]
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ccpA-motPS.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10376]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10948]
  
 
=== Additional information===
 
=== Additional information===
Line 58: Line 77:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' transcriptional regulator of carbon catabolite repression (CCR)
+
* '''Catalyzed reaction/ biological activity:''' L-glutamine + D-fructose 6-phosphate = L-glutamate + D-glucosamine 6-phosphate (according to Swiss-Prot)  
  
−
* '''Protein family:''' LacI family
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
−
 
−
=== Genes controlled by CcpA ===
 
−
 
−
* '''Activation by CcpA:''' ''[[pta]]'', ''[[ackA]]'', ''[[ilvB]]-[[ilvH]]-[[ilvC]]-[[leuA]]-[[leuB]]-[[leuC]]-[[leuD]]''
 
−
 
−
* '''Repression by CcpA:''' ''[[abbA]], [[amyE]]'', ''[[bglP]]-[[bglH]]'', ''[[bglS]]'', ''[[cccA]]'', ''[[citZ]]-[[icd]]-[[mdh]]'', ''[[levD]]-[[levE]]-[[levF]]-[[levG]]-[[sacC]]'', ''[[licB]]-[[licC]]-[[licA]]-[[licH]]'', ''[[phoP]]-[[phoR]]'', ''[[xylA]]-[[xylB]]'', ''[[xynP]]-[[xynB]]''
 
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 75: Line 88:
  
 
* '''Domains:'''  
 
* '''Domains:'''  
−
** HTH lacI-type Domain (1 – 58)
 
−
** DNA binding Domain  (6 – 25)
 
  
 
* '''Modification:'''
 
* '''Modification:'''
  
−
* '''Cofactor(s):''' [[PtsH |HPr]]-Ser46-P, Crh-Ser-46-P
+
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:'''glucose-6-phosphate, fructose-1,6-bisphosphate [http://www.ncbi.nlm.nih.gov/pubmed/17376479?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum Pubmed]
+
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' CcpA-[[PtsH |HPr]] [http://www.ncbi.nlm.nih.gov/pubmed/15369672?ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum PubMed], CcpA-[[Crh]] [http://www.ncbi.nlm.nih.gov/pubmed/16316990?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum PubMed]
+
* '''[[SubtInteract|Interactions]]:'''
  
−
* '''Localization:'''
+
* '''[[Localization]]:'''
 +
** cytoplasm (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [HELLO BSU00100]
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU00240&redirect=T BSU00240]
  
−
* '''Structure:''' CcpA-Crh-DNA-complex [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=52326 NCBI], complex with P-Ser-[[PtsH |HPr]] and sulphate ions [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=39857 NCBI]
+
* '''Structure:'''
 +
**[http://www.pdb.org/pdb/explore/explore.do?structureId=HIV2 HIV2] (from ''Bacillus subtilis'', 100% identity) {{PubMed|13454352}}
 +
** [http://www.pdb.org/pdb/explore/explore.do?structureId=2VF4 2VF4] (GlmS from ''E. coli'', 39% identity, 58% similarity) {{PubMed|18295797}}
 +
** the ribozyme: [http://www.rcsb.org/pdb/explore.do?structureId=3g8s 3G8S], [http://www.rcsb.org/pdb/explore.do?structureId=3G9C 3G9C], [http://www.rcsb.org/pdb/explore.do?structureId=3g8t 3G8T], [http://www.rcsb.org/pdb/explore.do?structureId=3g95 3G95], [http://www.rcsb.org/pdb/explore.do?structureId=3g96 3G96] (all for the ribozyme from ''Bacillus anthracis''), [http://www.rcsb.org/pdb/explore.do?structureId=2HO7 2HO7] (the ribozyme from ''Thermonanaerobacter tengcongensis'')
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P25144 P25144]
+
* '''UniProt:''' [http://www.uniprot.org/uniprot/P39754 P39754]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29740]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01780]
 +
 
 +
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.6.1.16 2.6.1.16]
  
 
=== Additional information===
 
=== Additional information===
  
 +
:* subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[ccpA]] [[motP]] [[motS]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16547058 PubMed]
+
* '''Operon:''' ''[[ybbP]]-[[ybbR]]-[[glmM]]-[[glmS]]''
 +
 
 +
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=glmS_200277_202079_1 glmS] {{PubMed|22383849}}
 +
 
 +
* '''Sigma factor:''' [[SigA]] {{PubMed|22211522}}
  
−
* '''Sigma factor:'''  
+
* '''Regulation:'''  
 +
** repressed by glucosamine, N-acetylglucosamine, N-propionylglucosamine or N-formylglucosamine {{PubMed|14343123}}
 +
** ''glmS'' is only expressed in the absence of glucosamine 6-phosphate ([[glmS]] [[ribozyme]])
  
−
* '''Regulation:''' constitutively  expressed [http://www.ncbi.nlm.nih.gov/sites/entrez/18757537 PubMed]
+
* '''Regulatory mechanism:''' ''glmS'' [[ribozyme]]: glucosamine 6-phosphate binds the leader mRNA, and a [[riboswitch]] with [[ribozyme]] activity cleaves off the ''[[glmS]]'' section from the mRNA, resulting in stopp of transcript elongation
  
−
* '''Additional information:''' there are about 3.000 molecules of CcpA per cell [http://www.ncbi.nlm.nih.gov/sites/entrez/8000527 PubMed]
+
* '''Additional information:'''  
 +
** subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
 +
** A [[ncRNA]] is predicted between ''[[glmM]]'' and ''[[glmS]]'' {{PubMed|20525796}}
 +
** number of protein molecules per cell (minimal medium with glucose and ammonium): 2000 {{PubMed|24696501}}
 +
** number of protein molecules per cell (complex medium with amino acids, without glucose): 4000 {{PubMed|24696501}}
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' QB5407 (spc), GP302 (erm), GP300 (an in frame deletion of ''[[ccpA]]''), available in [[Stülke]] lab
+
* '''Mutant:'''
  
−
* '''Expression vector:''' pGP643 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), available in [[Stülke]] lab
+
* '''Expression vector:'''
−
+
       
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''Antibody:''' available in [[Hillen]] and [[Stülke]] labs
+
* '''two-hybrid system:'''
 +
 
 +
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
  
−
[[Wolfgang Hillen]], Erlangen University, Germany [http://www.biologie.uni-erlangen.de/mibi/index2.html Homepage]
+
[[Wade Winkler]], University of Texas, USA, [http://www.utsouthwestern.edu/findfac/professional/0,,68018,00.html Homepage]
−
 
 
−
[[Richard Brennan]], Houston, Texas, USA [http://www.mdanderson.org/departments/biochem/display.cfm?id=556ef368-6c81-4043-b74f350d41dd06cb&method=displayfull&pn=a8427ebd-d0ff-11d4-80fd00508b603a14 Homepage]
 
−
 
 
−
[[Milton H. Saier]], University of California at San Diego, USA [http://biology.ucsd.edu/faculty/saier.html Homepage]
 
−
 
 
−
[[Yasutaro Fujita]], University of Fukuyama, Japan
 
−
 
 
−
[[Stülke|Jörg Stülke]], University of Göttingen, Germany [http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]
 
−
 
 
−
[[Oscar Kuipers]], University of Groningen, The Netherlands
 
−
[http://molgen.biol.rug.nl/molgen/index.php Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
  
 
=References=
 
=References=
 +
==Reviews==
 +
<pubmed> 18279655 </pubmed>
  
−
'''Reviews'''
+
==The ''glmS'' Ribozyme==
−
 
+
<pubmed>18079181 ,16484375, 16784238 ,15096624 , 16990543 ,17114942 ,16484375 , 15029187, 17283212 , 16298301, 19228039 21317896 21395279 </pubmed>
−
<pubmed> 8598282 , 19202299,14665673,18628769 ,18359269, 18628769    </pubmed>
 
−
 
 
−
'''General and physiological studies'''
 
−
 
 
−
<pubmed>1904524 ,10941796 ,12123463,8000527, 18757537,16547058,14523131 </pubmed>
 
−
 
 
−
'''Global analyses (proteome, transcriptome)'''
 
−
 
 
−
<pubmed>12850135 ,11251851,10559165, 11160890,17183215 </pubmed>
 
−
 
 
−
'''Repression of target genes by CcpA'''
 
−
 
 
−
<pubmed>15150224 ,16166551 ,11929549 , 7913927 ,17827291 ,11985717 ,12100558,7592486  </pubmed>
 
−
 
 
−
'''Positive regulation of gene expression by CcpA'''
 
−
 
 
−
<pubmed>8226682 ,12193635 ,10559153 ,15916605, 9811655 ,10986270 </pubmed>
 
−
 
 
−
'''Control of CcpA activity'''
 
−
 
 
−
<pubmed>7623661 ,9973552 ,9334231 ,12051938, 9689125 </pubmed>
 
−
 
 
−
'''CcpA-DNA interaction'''
 
−
 
 
−
<pubmed>8596444 ,10666464 ,15885105,7665492 ,9254709  </pubmed>
 
−
 
 
−
'''Functional analysis of CcpA'''
 
−
 
 
−
<pubmed>10383986 ,10601226 ,11557150,9252590 ,9988473  </pubmed>
 
−
 
 
−
'''Structural analyses'''
 
  
−
<pubmed>15369672 ,16316990 ,17376479 </pubmed>
+
==Other Original Publications==
 +
'''Additional publications:''' {{PubMed|22211522}}
 +
<pubmed> 14343123 17981983 ,11160890, 18295797 20525796  </pubmed>
 +
[[Category:Protein-coding genes]]

Latest revision as of 13:22, 29 July 2014

  • Description: glutamine-fructose-6-phosphate transaminase

Gene name glaube ich oder nicht glmS
Synonyms gcaA, ybxD
Essential yes PubMed
Product glutamine-fructose-6-phosphate transaminase
Function cell wall synthesis
Metabolic function and regulation of this protein in SubtiPathways:
sandbox
MW, pI 65 kDa, 4.796
Gene length, protein length 1800 bp, 600 aa
Immediate neighbours glmM, ybbU
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
File:Quintos.gif
This image was kindly provided by SubtiList
Genetic context
Test.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
GlmS expression.png
























Categories containing this gene/protein

cell wall synthesis, biosynthesis of cell wall components, essential genes

This gene is a member of the following regulons

glmS ribozyme

The gene

Basic information

  • Locus tag: BSU01780

Phenotypes of a mutant

essential PubMed

Database entries

  • BsubCyc: [HELLO BSU00100]
  • BsubCyc: "
  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: L-glutamine + D-fructose 6-phosphate = L-glutamate + D-glucosamine 6-phosphate (according to Swiss-Prot)
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:

Database entries

  • BsubCyc: [HELLO BSU00100]
  • BsubCyc: BSU00240
  • Structure:
    • HIV2 (from Bacillus subtilis, 100% identity) PubMed
    • 2VF4 (GlmS from E. coli, 39% identity, 58% similarity) PubMed
    • the ribozyme: 3G8S, 3G9C, 3G8T, 3G95, 3G96 (all for the ribozyme from Bacillus anthracis), 2HO7 (the ribozyme from Thermonanaerobacter tengcongensis)
  • KEGG entry: [2]

Additional information

  • subject to Clp-dependent proteolysis upon glucose starvation PubMed

Expression and regulation

  • Regulation:
    • repressed by glucosamine, N-acetylglucosamine, N-propionylglucosamine or N-formylglucosamine PubMed
    • glmS is only expressed in the absence of glucosamine 6-phosphate (glmS ribozyme)
  • Regulatory mechanism: glmS ribozyme: glucosamine 6-phosphate binds the leader mRNA, and a riboswitch with ribozyme activity cleaves off the glmS section from the mRNA, resulting in stopp of transcript elongation
  • Additional information:
    • subject to Clp-dependent proteolysis upon glucose starvation PubMed
    • A ncRNA is predicted between glmM and glmS PubMed
    • number of protein molecules per cell (minimal medium with glucose and ammonium): 2000 PubMed
    • number of protein molecules per cell (complex medium with amino acids, without glucose): 4000 PubMed

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Wade Winkler, University of Texas, USA, Homepage

Your additional remarks

References

Reviews


The glmS Ribozyme


Other Original Publications

Additional publications: PubMed

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