Difference between revisions of "Sandbox"

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−
* '''Description:''' "Catabolite repression HPr-like protein", Cofactor of the [[CcpA]] transcription factor<br/><br/>
+
* '''Description:''' similar to N-hydroxyarylamine O-acetyltransferase <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'''
−
|''crh''
+
|''yvcN''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvcM''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || catabolite repression HPr-like protein
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || catabolite repression
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 9,2 kDa, 4.70
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 5.582 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 255 bp, 85  amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 762 bp, 254 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvcL]]'', ''[[yvcN]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvcP]]'', ''[[crh]]''
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:crh_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yvcN_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 ===
  
−
* '''Coordinates:''' 3568325 - 3568579
+
* '''Coordinates:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 43: Line 43:
 
* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12403]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12404]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=The protein=
 
=The protein=
Line 53: Line 54:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' [[PtsH]],HPr family
+
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[PtsH |HPr]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 61: Line 62:
 
* '''Kinetic information:'''
 
* '''Kinetic information:'''
  
−
* '''Domains:''' HPr domain (1–85)
+
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylation on Ser46 by [[HPrK]] [http://www.ncbi.nlm.nih.gov/sites/entrez/9237995 PubMed]
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
Line 69: Line 70:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' Crh-[[GapA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed], Crh-[[CcpA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12972249 PubMed], [[HprK]]-Crh [http://www.ncbi.nlm.nih.gov/sites/entrez/12009882 PubMed]
+
* '''Interactions:'''
  
 
* '''Localization:'''
 
* '''Localization:'''
Line 75: Line 76:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=24634 NCBI], dimer [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=64943  NCBI], CcpA-Crh-DNA complex [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=52326  NCBI], dimeric phosphor-Crh [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=39567 NCBI]
+
* '''Structure:'''
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O06976]
+
 
 +
* '''Swiss prot entry:'''
 +
 
 +
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU34730]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU34740]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
−
 
−
Crh does not possess the phosphorylation site used for PTS phosphotransfer (His-15 in [[PtsH]]), it can only be phosphorylated on Ser-46
 
  
 
=Expression and regulation=
 
=Expression and regulation=
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* '''Operon:''' ''[[yvcI]]-[[yvcJ]]-[[yvcK]]-[[yvcL]]-[[crh]]-[[yvcN]]''  [http://www.ncbi.nlm.nih.gov/sites/entrez/9237995 PubMed]
 
* '''Operon:''' ''[[yvcI]]-[[yvcJ]]-[[yvcK]]-[[yvcL]]-[[crh]]-[[yvcN]]''  [http://www.ncbi.nlm.nih.gov/sites/entrez/9237995 PubMed]
  
−
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16272399 PubMed]
+
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16272399 PubMed]
  
 
* '''Regulation:''' very weak stimuation of expression by citrate and succinate [http://www.ncbi.nlm.nih.gov/sites/entrez/16272399 PubMed]
 
* '''Regulation:''' very weak stimuation of expression by citrate and succinate [http://www.ncbi.nlm.nih.gov/sites/entrez/16272399 PubMed]
Line 94: Line 96:
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:''' Crh is weakly expressed. This results in part from a poorly conserved ribosomal binding site of the mRNA. [http://www.ncbi.nlm.nih.gov/sites/entrez/15126459 PubMed]
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP860 (aphA3), QB7097 (spc), available in [[Stülke]] lab
+
* '''Mutant:'''
  
−
* '''Expression vector:''' pGP641 (in [[pGP380]], for SPINE, expression in ''B. subtilis''), pGP734 (in [[pGP380]], for SPINE, expression in ''B. subtilis''), available in [[Stülke]] lab
+
* '''Expression vector:'''
−
+
       
−
* '''lacZ fusion:''' see ''[[yvcI]]''
+
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Boris Görke| Görke]] lab
+
* '''two-hybrid system:'''  
  
−
* '''Antibody:''' available in [[Stülke]] lab (not very good)
+
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Boris Görke]], University of Göttingen, Germany
 
−
[http://wwwuser.gwdg.de/~genmibio/goerke.html Homepage]
 
−
 
−
[[Anne Galinier]], University of Marseille, France
 
−
 
−
[[Wolfgang Hillen]], Erlangen University, Germany [http://www.biologie.uni-erlangen.de/mibi/index2.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]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 125: Line 118:
 
=References=
 
=References=
  
−
# Juy M, Penin F, Favier A (2003) Dimerization of Crh by reversible 3D domain swapping induces structural adjustments to its monomeric homologue Hpr. ''J Mol Biol.'' '''332(4):'''767-76. [http://www.ncbi.nlm.nih.gov/sites/entrez/12972249 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]
−
# Galinier A, Deutscher J, Martin-Verstraete I: Phosphorylation of either Crh or HPr mediates binding of CcpA to the ''Bacillus subtilis xyn cre'' and catabolite repression of the ''xyn'' operon. J Mol Biol 1999, 286:307-314. [http://www.ncbi.nlm.nih.gov/sites/entrez/9973552 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]
 
 
# 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]
 
# 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]
−
# Görke, B., Fraysse, L. & Galinier, A. Drastic differences in Crh and HPr synthesis levels reflect their different impacts on catabolite repression in ''Bacillus subtilis''. J. Bacteriol. 186, 2992-2995 (2004). [http://www.ncbi.nlm.nih.gov/sites/entrez/15126459 PubMed]
 
−
# Martin-Verstraete, I., Deutscher, J., and Galinier, A. (1999) Phosphorylation of HPr and Crh by HprK, early steps in the catabolite repression signalling pathway for the ''Bacillus subtilis'' levanase operon. J Bacteriol 181: 2966-2969. [http://www.ncbi.nlm.nih.gov/sites/entrez/10217795 PubMed]
 
−
# Pompeo ''et al.'' (2007) Interaction of GapA with HPr and its homologue, Crh: Novel levels of regulation of a key step of glycolysis in ''Bacillus subtilis''? J Bacteriol 189, 1154-1157.[http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed]
 
−
# Schumacher, M. A., Seidel, G., Hillen, W. & Brennan, R. G. Phosphoprotein Crh-Ser46-P displays altered binding to CcpA to effect carbon catabolite regulation. J. Biol. Chem. 281, 6793-6800 (2006). [http://www.ncbi.nlm.nih.gov/sites/entrez/16316990 PubMed]
 

Revision as of 17:38, 15 April 2009

  • Description: similar to N-hydroxyarylamine O-acetyltransferase

Gene name yvcN
Synonyms
Essential no
Product unknown
Function unknown
MW, pI 28 kDa, 5.582
Gene length, protein length 762 bp, 254 aa
Immediate neighbours yvcP, crh
Hier soll was neues rein
Genetic context
YvcN context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

  • Structure:
  • Swiss prot entry:
  • 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:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

  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
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