Difference between revisions of "Sandbox"

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−
* '''Description:''' acetoin ABC transporter  (substrate-binding lipoprotein) <br/><br/>
+
* '''Description:''' phosphoenolpyruvate carboxykinase <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'''
−
|''ytrF''
+
|''pckA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ppc''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || acetoin ABC transporter  (substrate-binding lipoprotein)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || phosphoenolpyruvate carboxykinase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || uptake of acetoin
+
|style="background:#ABCDEF;" align="center"|'''Function''' || synthesis of phosphoenolpyruvate
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 8.292 
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 58,1 kDa, 5.12
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1308 bp, 436 aa
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1581 bp, 527 amino acids
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[bceR]]'', ''[[ytrE]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[metK]]'', ''[[ytmB]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15019&#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:CAB15034&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ytrF_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:pckA_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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<br/><br/>
 
<br/><br/>
 +
  
 
=The gene=
 
=The gene=
Line 35: Line 38:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:'''
+
* '''Coordinates:''' 3128579 - 3130159
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 44:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ytrABCDEF.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pckA.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13916]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11841]
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=The protein=
 
=The protein=
Line 52: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' ATP + oxaloacetate = ADP + phosphoenolpyruvate + CO(2)
  
−
* '''Protein family:'''
+
* '''Protein family:''' phosphoenolpyruvate carboxykinase [ATP] family
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Domains:'''  
 
* '''Domains:'''  
 +
** Nucleotide binding Domain (233–240)
  
 
* '''Modification:'''
 
* '''Modification:'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' Cytoplasm
+
* '''Localization:''' Cytoplasm cytoplasm
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2PXZ 2PXZ] (''E.coli'')
  
−
* '''Swiss prot entry:'''
+
* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P54418]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU30410]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU30560]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.ch/cgi-bin/get-enzyme-entry?4.1.1.49 4.1.1.49]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=Expression and regulation=
 
=Expression and regulation=
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* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:'''  
+
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+15720552 PubMed]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' repressed by glucose (7-fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  repressed (35-times) Glc, repressor [[CcpN]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+15720552 PubMed]
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' transcription repression
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
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* '''Expression vector:'''
 
* '''Expression vector:'''
−
       
+
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
−
 
−
* '''two-hybrid system:'''
 
  
 
* '''Antibody:'''
 
* '''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
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 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]
 +
# 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 03:18, 30 April 2009

  • Description: phosphoenolpyruvate carboxykinase

Gene name pckA
Synonyms ppc
Essential no
Product phosphoenolpyruvate carboxykinase
Function synthesis of phosphoenolpyruvate
MW, pI 58,1 kDa, 5.12
Gene length, protein length 1581 bp, 527 amino acids
Immediate neighbours metK, ytmB
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
PckA context.gif
This image was kindly provided by SubtiList




The gene

Basic information

  • Coordinates: 3128579 - 3130159

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: ATP + oxaloacetate = ADP + phosphoenolpyruvate + CO(2)
  • Protein family: phosphoenolpyruvate carboxykinase [ATP] family
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
    • Nucleotide binding Domain (233–240)
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: Cytoplasm cytoplasm

Database entries

  • Structure: 2PXZ (E.coli)
  • Swiss prot entry: [3]
  • KEGG entry: [4]

Additional information

Expression and regulation

  • Operon:
  • Regulation: repressed by glucose (7-fold) PubMed, repressed (35-times) Glc, repressor CcpN PubMed
  • Regulatory mechanism: transcription repression
  • 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. Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab Eng. 5: 133-149 PubMed
  2. 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
  3. Tännler et al. (2008) CcpN controls central carbon fluxes in Bacillus subtilis. J. Bacteriol. 190: 6178-6187. PubMed
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