Difference between revisions of "Sandbox"

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−
* '''Description:''' unknown <br/><br/>
+
* '''Description:''' nucleotide-binding protein <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'''
−
|''yvbI''
+
|''yvcJ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Product''' || nucleotide-binding P-loop-containing protein
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+
|style="background:#ABCDEF;" align="center"|'''Function''' || required for the expression of late competence genes
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 25 kDa, 7.759  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 6.702  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 696 bp, 232 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 885 bp, 295 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvbH]]'', ''[[yvbJ]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvcK]]'', ''[[yvcI]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15392&#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:CAB15482&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yvbI_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yvcJ_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>
 
|-
 
|-
Line 35: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU33870
+
* '''Locus tag:''' BSU34770
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
reduced competence  [http://www.ncbi.nlm.nih.gov/sites/entrez/19074378 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
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* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14082]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12400]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' binds and hydrolyzes nucleotides, required for the expression of late competence genes (''[[comK]], [[comS]]'')  [http://www.ncbi.nlm.nih.gov/sites/entrez/19074378 PubMed]
  
−
* '''Protein family:'''
+
* '''Protein family:''' UPF0042 family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' cell membrane (according to Swiss-Prot),  membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O32246 O32246]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O06973 O06973]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33870]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU34770]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[yvcI]]-[[yvcJ]]-[[yvcK]]-[[yvcL]]-[[crh]]-[[yvcN]]''  [http://www.ncbi.nlm.nih.gov/sites/entrez/9237995 PubMed]
  
−
* '''[[[[Sigma factor]]]]:'''  
+
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16272399 PubMed]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' very weak stimuation of expression by citrate and succinate [http://www.ncbi.nlm.nih.gov/sites/entrez/16272399 PubMed]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 102: Line 104:
 
* '''Mutant:'''
 
* '''Mutant:'''
  
−
* '''Expression vector:'''
+
* '''Expression vector:''' pGP735 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), available in [[Stülke]] lab
 
          
 
          
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
Line 113: Line 115:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Anne Galinier]], University of Marseille, France
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 118: Line 122:
 
=References=
 
=References=
  
−
<pubmed>18763711, </pubmed>
+
<pubmed>9237995 16272399 19074378, </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]
+
# Galinier, A., Haiech, J., Kilhoffer, M.-C., Jaquinod, M., Stülke, J., Deutscher, J., & Martin-Verstraete, I. (1997) The Bacillus subtilis crh gene encodes a HPr-like protein involved in carbon catabolite repression. Proc. Natl. Acad. Sci. USA 94: 8439-8444. [http://www.ncbi.nlm.nih.gov/sites/entrez/9237995 PubMed]
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
# Görke et al. (2005) YvcK of ''Bacillus subtilis'' is required for a normal cell shape and for growth on Krebs cycle intermediates and substrates of the pentose phosphate pathway. Microbiology 151: 3777-3791. [http://www.ncbi.nlm.nih.gov/sites/entrez/16272399 PubMed]
 +
# Luciano , J., E. Foulquier, J.-R. Fantino, A. Galinier, and F. Pompeo (2009) Characterization of YvcJ, a conserved P-loop-containing protein, and Its implication in competence in ''Bacillus subtilis''. J. Bacteriol. 191: 1556-1564-3791. [http://www.ncbi.nlm.nih.gov/sites/entrez/19074378 PubMed]

Revision as of 13:51, 8 June 2009

  • Description: nucleotide-binding protein

Gene name yvcJ
Synonyms
Essential no
Product nucleotide-binding P-loop-containing protein
Function required for the expression of late competence genes
MW, pI 33 kDa, 6.702
Gene length, protein length 885 bp, 295 aa
Immediate neighbours yvcK, yvcI
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YvcJ context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU34770

Phenotypes of a mutant

reduced competence PubMed

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: binds and hydrolyzes nucleotides, required for the expression of late competence genes (comK, comS) PubMed
  • Protein family: UPF0042 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:

Database entries

  • Structure:
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation: very weak stimuation of expression by citrate and succinate PubMed
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector: pGP735 (N-terminal Strep-tag, purification from B. subtilis, for SPINE, in pGP380), available in Stülke lab
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Anne Galinier, University of Marseille, France

Your additional remarks

References

Jennifer Luciano, Elodie Foulquier, Jean-Raphael Fantino, Anne Galinier, Frédérique Pompeo
Characterization of YvcJ, a conserved P-loop-containing protein, and its implication in competence in Bacillus subtilis.
J Bacteriol: 2009, 191(5);1556-64
[PubMed:19074378] [WorldCat.org] [DOI] (I p)

Boris Görke, Elodie Foulquier, Anne Galinier
YvcK of Bacillus subtilis is required for a normal cell shape and for growth on Krebs cycle intermediates and substrates of the pentose phosphate pathway.
Microbiology (Reading): 2005, 151(Pt 11);3777-3791
[PubMed:16272399] [WorldCat.org] [DOI] (P p)

A Galinier, J Haiech, M C Kilhoffer, M Jaquinod, J Stülke, J Deutscher, I Martin-Verstraete
The Bacillus subtilis crh gene encodes a HPr-like protein involved in carbon catabolite repression.
Proc Natl Acad Sci U S A: 1997, 94(16);8439-44
[PubMed:9237995] [WorldCat.org] [DOI] (P p)

  1. Galinier, A., Haiech, J., Kilhoffer, M.-C., Jaquinod, M., Stülke, J., Deutscher, J., & Martin-Verstraete, I. (1997) The Bacillus subtilis crh gene encodes a HPr-like protein involved in carbon catabolite repression. Proc. Natl. Acad. Sci. USA 94: 8439-8444. PubMed
  2. Görke et al. (2005) YvcK of Bacillus subtilis is required for a normal cell shape and for growth on Krebs cycle intermediates and substrates of the pentose phosphate pathway. Microbiology 151: 3777-3791. PubMed
  3. Luciano , J., E. Foulquier, J.-R. Fantino, A. Galinier, and F. Pompeo (2009) Characterization of YvcJ, a conserved P-loop-containing protein, and Its implication in competence in Bacillus subtilis. J. Bacteriol. 191: 1556-1564-3791. PubMed
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