Difference between revisions of "Sandbox"

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−
* '''Description:''' transcriptional repressor of gluconeogenetic genes and of [[sr1]]. repression in the presence of glucose <br/><br/>
+
* '''Description:''' Modulator of CcpN activity<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'''
−
|''ccpN''
+
|''yqfL''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqzB ''
+
|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''' || transcriptional regulator
+
|style="background:#ABCDEF;" align="center"| '''Product''' || modulator of [[CcpN]] activity
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || repressor of genes involved in <br/>gluconeogenesis (''[[gapB]]'','' [[pckA]]'') and of ''[[sr1]]''
+
|style="background:#ABCDEF;" align="center"|'''Function''' || inhibits [[CcpN]] activity
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23.4 kDa, 7.22
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30,4 kDa, 5.78
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 636 bp, 212 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 810 bp, 270 amino acids
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqfL]]'', ''[[glyS]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqxD]]'', ''[[ccpN]]''
 
|-
 
|-
 
|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:yqzB_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yqfL_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 29: Line 29:
 
__TOC__
 
__TOC__
  
−
<br/><br/><br/>
+
<br/><br/>
  
  
Line 36: Line 36:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:''' 2604195 - 2604830
+
* '''Coordinates:''' 2603357 - 2604166
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
Impaired growth on glucose due to re-routing of carbon from glycolysis to the pentose phosphate pathway [http://www.ncbi.nlm.nih.gov/sites/entrez/18586936 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
Line 45: Line 44:
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ccpN-yqfL.html]
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ccpN-yqfL.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13768]
+
* '''SubtiList entry:'''[http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11659]
  
 
=== Additional information===
 
=== Additional information===
Line 53: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' transcription repression of the ''[[gapB]]'', ''[[pckA]]'', and ''[[sr1]]'' genes in the presence of glucose [http://www.ncbi.nlm.nih.gov/sites/entrez/2548995 PubMed]
+
* '''Catalyzed reaction/ biological activity:''' negative effector of [[CcpN]] activity [http://www.ncbi.nlm.nih.gov/sites/entrez/15720552 PubMed]
  
−
* '''Protein family:'''
+
* '''Protein family:''' pyruvate, phosphate dikinase regulatory protein family
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 63: Line 62:
 
* '''Kinetic information:'''
 
* '''Kinetic information:'''
  
−
* '''Domains:'''  
+
* '''Domains:''' nucleotide binding domain (ATP) (151–158)
  
 
* '''Modification:'''
 
* '''Modification:'''
Line 69: Line 68:
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:'''  
+
* '''Effectors of protein activity:'''
−
** [[YqfL]] (negative effector of CcpN activity) [http://www.ncbi.nlm.nih.gov/sites/entrez/15720552 PubMed]
 
−
** ATP enhances CcpN-dependent repression, ADP counteracts the repressing activity of CcpN [http://www.ncbi.nlm.nih.gov/sites/entrez/18511073 PubMed]
 
  
 
* '''Interactions:'''
 
* '''Interactions:'''
Line 81: Line 78:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O34994]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P54470]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU25250]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU25240]
 +
 
 +
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.-.- 2.7.-.-]
  
 
=== Additional information===
 
=== Additional information===
Line 94: Line 93:
 
* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' constitutively expressed [http://www.ncbi.nlm.nih.gov/sites/entrez/15720552 PubMed]
+
* '''Regulation:''' constitutive [http://www.ncbi.nlm.nih.gov/sites/entrez/15720552 PubMed]
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 100: Line 99:
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' DB104 ''ccpN''::[[cat]], available in [[Sabine Brantl]] lab
+
* '''Mutant:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
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* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''Antibody:''' available in [[Sabine Brantl]] lab
+
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
 
[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France
 
[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France
  
−
[[Sabine Brantl |Sabine Brantl]], Bacterial Genetics, Friedrich-Schiller-University of Jena, Germany [http://www.uni-jena.de/AG_Bakteriengenetik_(_Doz__Dr__Sabine_Brantl_).html homepage]
 
  
−
[[Uwe Sauer]], ETH Zürich, Switzerland [http://www.imsb.ethz.ch/researchgroup/sauer homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
  
 
=References=
 
=References=
−
 
  
 
# Servant et al. (2005) CcpN (YqzB), a novel regulator for CcpA-independent catabolite repression of ''Bacillus subtilis'' gluconeogenic genes. Mol. Microbiol. 55: 1435-1451. [http://www.ncbi.nlm.nih.gov/sites/entrez/15720552 PubMed]
 
# Servant et al. (2005) CcpN (YqzB), a novel regulator for CcpA-independent catabolite repression of ''Bacillus subtilis'' gluconeogenic genes. Mol. Microbiol. 55: 1435-1451. [http://www.ncbi.nlm.nih.gov/sites/entrez/15720552 PubMed]
−
# Licht et al. (2005) Implication of CcpN in the regulation of a novel untranslated RNA (SR1) in ''Bacillus subtilis''. Mol. Microbiol. 58: 189-206. [http://www.ncbi.nlm.nih.gov/sites/entrez/16164558 PubMed]
 
−
# Licht & Brantl (2006) Transcriptional repressor CcpN from ''Bacillus subtilis'' compensates asymmetric contact distribution by cooperative binding. J. Mol. Biol. 364: 434-448. [http://www.ncbi.nlm.nih.gov/sites/entrez/17011578 PubMed]
 
−
# Licht et al. (2008) Identification of ligands affecting the activity of the transcriptional repressor CcpN from ''Bacillus subtilis''. J. Mol. Biol. 380: 17-30. [http://www.ncbi.nlm.nih.gov/sites/entrez/18511073 PubMed]
 
−
# Tännler et al. (2008) CcpN controls central carbon fluxes in ''Bacillus subtilis''. J. Bacteriol. 190: 6178-6187. [http://www.ncbi.nlm.nih.gov/sites/entrez/18586936 PubMed]
 

Revision as of 18:45, 15 April 2009

  • Description: Modulator of CcpN activity

Gene name yqfL
Synonyms
Essential no
Product modulator of CcpN activity
Function inhibits CcpN activity
MW, pI 30,4 kDa, 5.78
Gene length, protein length 810 bp, 270 amino acids
Immediate neighbours yqxD, ccpN
Hier soll was neues rein
Genetic context
YqfL context.gif
This image was kindly provided by SubtiList




The gene

Basic information

  • Coordinates: 2603357 - 2604166

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: negative effector of CcpN activity PubMed
  • Protein family: pyruvate, phosphate dikinase regulatory protein family
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains: nucleotide binding domain (ATP) (151–158)
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • Structure:
  • Swiss prot entry: [3]
  • KEGG entry: [4]

Additional information

Expression and regulation

  • Regulation: constitutive PubMed
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • Antibody:

Labs working on this gene/protein

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


Your additional remarks

References

  1. Servant et al. (2005) CcpN (YqzB), a novel regulator for CcpA-independent catabolite repression of Bacillus subtilis gluconeogenic genes. Mol. Microbiol. 55: 1435-1451. PubMed
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