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/>
  
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{| align="right" border="1" cellpadding="2"
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|-
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|style="background:#ABCDEF;" align="center"|'''Gene name'''
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|''ccpN''
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|-
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqzB ''
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|-
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no
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|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator
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|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || repressor of genes involved in gluconeogenesis (''[[gapB]]'','' [[pckA]]'') and of ''[[sr1]]''
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|-
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23.4 kDa, 7.22
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|-
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 636 bp, 212 amino acids
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|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[glyS]]'', ''[[yqfL]]''
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|-
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ccpN_nucleotide.txt    Gene sequence      (+200bp)  ]'''
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ccpN_protein.txt Protein sequence]'''
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|-
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|colspan="2" | '''Genetic context''' <br/> [[Image:yqzB_context.gif]]
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|-
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|}
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__TOC__
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<br/><br/>
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=The gene=
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=== Basic information ===
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* '''Coordinates:''' 2604195 - 2604830
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===Phenotypes of a mutant ===
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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]
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=== Database entries ===
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* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ccpN-yqfL.html]
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* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13768]
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=== Additional information===
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=== Basic information/ Evolution ===
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* '''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]
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* '''Protein family:'''
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* '''Paralogous protein(s):'''
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=== Extended information on the protein ===
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* '''Kinetic information:'''
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* '''Domains:'''
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* '''Modification:'''
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* '''Cofactor(s):'''
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* '''Effectors of protein activity:'''
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** [[YqfL]] (negative effector of CcpN activity) [http://www.ncbi.nlm.nih.gov/sites/entrez/15720552 PubMed]
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** ATP enhances CcpN-dependent repression, ADP counteracts the repressing activity of CcpN [http://www.ncbi.nlm.nih.gov/sites/entrez/18511073 PubMed]
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* '''Interactions:'''
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* '''Localization:'''
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=== Database entries ===
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* '''Structure:'''
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* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O34994]
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* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU25250]
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=== Additional information===
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=Expression and regulation=
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* '''Operon:''' ''[[ccpN]]''-''[[yqfL]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/15720552 PubMed]
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* '''Sigma factor:'''
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* '''Regulation:''' constitutively expressed [http://www.ncbi.nlm.nih.gov/sites/entrez/15720552 PubMed]
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* '''Additional information:'''
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=Biological materials =
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* '''Mutant:''' DB104 ''ccpN''::[[cat]], available in [[Sabine Brantl]] lab
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* '''Expression vector:'''
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* '''lacZ fusion:'''
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* '''GFP fusion:'''
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* '''Antibody:''' available in [[Sabine Brantl]] lab
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=Labs working on this gene/protein=
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[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France
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[[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]
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=Your additional remarks=
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=References=
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# 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]
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# 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]
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# 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]
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# 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]
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# 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 15:23, 10 February 2009

  • Description: transcriptional repressor of gluconeogenetic genes and of sr1. repression in the presence of glucose

Gene name ccpN
Synonyms yqzB
Essential no
Product transcriptional regulator
Function repressor of genes involved in gluconeogenesis (gapB, pckA) and of sr1
MW, pI 23.4 kDa, 7.22
Gene length, protein length 636 bp, 212 amino acids
Immediate neighbours glyS, yqfL
Gene sequence (+200bp) Protein sequence
Genetic context
YqzB context.gif




The gene

Basic information

  • Coordinates: 2604195 - 2604830

Phenotypes of a mutant

Impaired growth on glucose due to re-routing of carbon from glycolysis to the pentose phosphate pathway PubMed

Database entries

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

Additional information

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: transcription repression of the gapB, pckA, and sr1 genes in the presence of glucose PubMed
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
    • YqfL (negative effector of CcpN activity) PubMed
    • ATP enhances CcpN-dependent repression, ADP counteracts the repressing activity of CcpN PubMed
  • Interactions:
  • Localization:

Database entries

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

Additional information

Expression and regulation

  • Sigma factor:
  • Regulation: constitutively expressed PubMed
  • Additional information:

Biological materials

  • Expression vector:
  • lacZ fusion:
  • GFP fusion:

Labs working on this gene/protein

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

Sabine Brantl, Bacterial Genetics, Friedrich-Schiller-University of Jena, Germany homepage

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
  2. Licht et al. (2005) Implication of CcpN in the regulation of a novel untranslated RNA (SR1) in Bacillus subtilis. Mol. Microbiol. 58: 189-206. PubMed
  3. Licht & Brantl (2006) Transcriptional repressor CcpN from Bacillus subtilis compensates asymmetric contact distribution by cooperative binding. J. Mol. Biol. 364: 434-448. PubMed
  4. Licht et al. (2008) Identification of ligands affecting the activity of the transcriptional repressor CcpN from Bacillus subtilis. J. Mol. Biol. 380: 17-30. PubMed
  5. Tännler et al. (2008) CcpN controls central carbon fluxes in Bacillus subtilis. J. Bacteriol. 190: 6178-6187. PubMed
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