Difference between revisions of "Sandbox"

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* '''Description:''' cytochrome-c oxidase (subunit I) <br/><br/>
+
* '''Description:''' pleiotropic regulator of sulphur metabolism <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'''
−
|''ctaD''
+
|''cymR ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yrzC''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/17114254 PubMed]
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || cytochrome-c oxidase (subunit I)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || transcription repressor
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || respiration
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of sulphur metabolism
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 68 kDa, 6.985  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 11 kDa, 9.879  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1866 bp, 622 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 333 bp, 111 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ctaC]]'', ''[[ctaE]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yrvO]]'', ''[[yrvN]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13363&#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:CAB14694&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yrzC_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ctaD_context.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>
 
|-
 
|-
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU14900
+
* '''Locus tag:''' BSU27520
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
essential [http://www.ncbi.nlm.nih.gov/pubmed/17114254 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ctaBCDEFG.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cymR-yrvO-trmU.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10216]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13813]
  
 
=== Additional information===
 
=== Additional information===
Line 56: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' 4 ferrocytochrome c + O<sub>2</sub> + 4 H<sup>+</sup> = 4 ferricytochrome c + 2 H<sub>2</sub>O (according to Swiss-Prot)
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' heme-copper respiratory oxidase family (according to Swiss-Prot)
+
* '''Protein family:''' Rrf2 family of transcription regulators
  
−
* '''Paralogous protein(s):''' [[QoxB]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Modification:'''
 
* '''Modification:'''
  
−
* '''Cofactor(s):'''
+
* '''Cofactor(s):''' [[CysK]] acts as corepressor [http://www.ncbi.nlm.nih.gov/sites/entrez/18974048 PubMed]
  
−
* '''Effectors of protein activity:'''
+
* '''Effectors of protein activity:'''  
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[CymR]]-[[CysK]], the complex is formed in the presence of cysteine, and results in DNA binding and repression of genes of cysteine biosynthesis [http://www.ncbi.nlm.nih.gov/sites/entrez/18974048 PubMed]
  
−
* '''Localization:''' cell membrane (according to Swiss-Prot)
+
* '''Localization:''' cytoplasm (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P24010 P24010]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O34527 O34527]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14900]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU27520]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.9.3.1 1.9.3.1]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[cymR]]-[[yrvO]]-[[trmU]]''
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigA]]
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
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* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 117: Line 113:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Isabelle Martin-Verstraete]], Institute Pasteur, Paris, France
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 122: Line 120:
 
=References=
 
=References=
  
−
<pubmed>17114254, </pubmed>
+
<pubmed>18974048 16513748, </pubmed>
−
# Thomaides, H. B., Davison, E. J., Burston, L., Johnson, H., Brown, D. R., Hunt, A. C., Errington, J., and Czaplewski, L. (2007) Essential bacterial functions encoded by gene pairs. J Bacteriol 189, 591-602. [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 PubMed]
+
# Tanous et al. (2008) The CymR regulator in complex with the enzyme CysK controls cysteine metabolism in ''Bacillus subtilis''.''J. Biol. Chem.'' '''283:''' 35551-35560. [http://www.ncbi.nlm.nih.gov/sites/entrez/18974048 PubMed]
 +
# Even S., Burguiere P., Auger S., Soutourina O., Danchin A., Martin-Verstraete I. (2006) Global control of cysteine metabolism by CymR in Bacillus subtilis. ''J. Bacteriol'' '''188:''' 2184-2197  [http://www.ncbi.nlm.nih.gov/sites/entrez/16513748 PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [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]

Revision as of 13:14, 8 June 2009

  • Description: pleiotropic regulator of sulphur metabolism

Gene name cymR
Synonyms yrzC
Essential no
Product transcription repressor
Function regulation of sulphur metabolism
MW, pI 11 kDa, 9.879
Gene length, protein length 333 bp, 111 aa
Immediate neighbours yrvO, yrvN
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YrzC context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU27520

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family: Rrf2 family of transcription regulators
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Effectors of protein activity:
  • Interactions: CymR-CysK, the complex is formed in the presence of cysteine, and results in DNA binding and repression of genes of cysteine biosynthesis PubMed
  • Localization: cytoplasm (according to Swiss-Prot)

Database entries

  • Structure:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Isabelle Martin-Verstraete, Institute Pasteur, Paris, France

Your additional remarks

References

Catherine Tanous, Olga Soutourina, Bertrand Raynal, Marie-Françoise Hullo, Peggy Mervelet, Anne-Marie Gilles, Philippe Noirot, Antoine Danchin, Patrick England, Isabelle Martin-Verstraete
The CymR regulator in complex with the enzyme CysK controls cysteine metabolism in Bacillus subtilis.
J Biol Chem: 2008, 283(51);35551-60
[PubMed:18974048] [WorldCat.org] [DOI] (P p)

Sergine Even, Pierre Burguière, Sandrine Auger, Olga Soutourina, Antoine Danchin, Isabelle Martin-Verstraete
Global control of cysteine metabolism by CymR in Bacillus subtilis.
J Bacteriol: 2006, 188(6);2184-97
[PubMed:16513748] [WorldCat.org] [DOI] (P p)

  1. Tanous et al. (2008) The CymR regulator in complex with the enzyme CysK controls cysteine metabolism in Bacillus subtilis.J. Biol. Chem. 283: 35551-35560. PubMed
  2. Even S., Burguiere P., Auger S., Soutourina O., Danchin A., Martin-Verstraete I. (2006) Global control of cysteine metabolism by CymR in Bacillus subtilis. J. Bacteriol 188: 2184-2197 PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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