Difference between revisions of "Sandbox"

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−
* '''Description:''' repressor of the glycolytic ''[[gapA]]'' operon<br/><br/>
+
* '''Description:''' pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit) <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'''
−
|''cggR''
+
|''pdhC''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvbQ ''
+
|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''' || central glycolytic genes regulator
+
|style="background:#ABCDEF;" align="center"| '''Product''' || pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || transcriptional regulator
+
|style="background:#ABCDEF;" align="center"|'''Function''' || links glycolysis and TCA cycle
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 37,2 kDa,5.68
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 4.855 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1020 bp, 340 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1326 bp, 442 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[araE]]'', ''[[gapA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pdhB]]'', ''[[pdhD]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/cggR_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pdhC_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/cggR_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pdhC_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:cggR_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:pdhC_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 31: Line 31:
  
 
<br/><br/>
 
<br/><br/>
−
 
  
 
=The gene=
 
=The gene=
Line 37: Line 36:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:''' 3481786 - 3482805
+
* '''Coordinates:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
defects in sporulation and unable to grow on glucose as single carbon source [http://www.ncbi.nlm.nih.gov/pubmed/11976308 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pdhABCD.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14085]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10209]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=The protein=
 
=The protein=
Line 53: Line 55:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' transcription repression of the glycolytic ''[[gapA]]'' operon
+
* '''Catalyzed reaction/ biological activity:'''  
  
 
* '''Protein family:'''
 
* '''Protein family:'''
Line 64: Line 66:
  
 
* '''Domains:'''  
 
* '''Domains:'''  
−
** DNA binding domain (H-T-H motif) (37–56)
 
  
 
* '''Modification:'''
 
* '''Modification:'''
Line 70: Line 71:
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:''' fructose 1.6-bisphosphate [http://www.ncbi.nlm.nih.gov/sites/entrez/12622823 PubMed] and dihydroxyacetone phosphate, glucose-6-phosphate and fructose-6-phosphate [http://www.ncbi.nlm.nih.gov/sites/entrez/18554327 PubMed] act as inducer and result in release of CggR from the DNA
+
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[PdhA]]-[[PdhB]]-[[PdhC]]-[[PdhD]]
  
−
* '''Localization:'''
+
* '''Localization:''' membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' complex with Fructose-6-Phosphate [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=65242 NCBI], effector binding domain [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=44226 NCBI]
+
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1W88 1W88] (E1 in complex with subunit binding domain of E2, ''Geobacillus stearothermophilus''), [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2PDE 2PDE] (peripheral subunit binding domain, ''Geobacillus stearothermophilus''), [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1LAC 1LAC] (lipoyl domain, ''Geobacillus stearothermophilus''), [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1B5S 1B5S] (catalytic domain (residues 184-425) , ''Geobacillus stearothermophilus'')
 +
* '''Swiss prot entry:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O32253]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14600]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33950]
+
* '''E.C. number:''' 2.3.1.12
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[pdhA]]-[[pdhB]]-[[pdhC]]-[[pdhD]]''
−
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]''
 
−
** ''[[cggR]]-[[gapA]]''
 
  
−
The primary mRNAs of the operon are highly unstable. The primary mRNA is subject to processing at the very end of the ''[[cggR]]'' open reading frame. This results in stable mature ''[[gapA]]'' and ''[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' mRNAs. The processing event requires the [[Rny]] protein.
+
* '''Sigma factor:''' [[SigA]]
  
−
* '''Sigma factor:''' [[SigA]]  
+
* '''Regulation:''' expression activated by glucose (1.94) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  weak induction by glucose [http://www.ncbi.nlm.nih.gov/sites/entrez/12850135 PubMed]
  
−
* '''Regulation:''' expression activated by glucose (76.76) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  [[CggR]] represses the operon in the absence of glycolytic sugars [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12622823 PubMed]
+
* '''Regulatory mechanism:'''  
−
 
 
−
* '''Regulatory mechanism:''' repression
 
−
 
 
−
* '''Database entries:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html DBTBS]
 
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 107: Line 102:
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP311 (in frame deletion), available in [[Stülke]] lab
+
* '''Mutant:'''
  
−
* '''Expression vector:''' pGP705 (N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab
+
* '''Expression vector:'''
−
+
       
−
* '''lacZ fusion:''' pGP504 (in [[pAC7]]), pGP509 (in [[pAC6]]), available in [[Stülke]] lab
+
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''Antibody:''' available in [[Stülke]] lab
+
* '''two-hybrid system:'''
 +
 
 +
* '''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=
  
 
=References=
 
=References=
−
hier steht Paper
+
 
−
# Commichau, F. M., Rothe, F. M., Herzberg, C., Wagner, E., Hellwig, D., Lehnik-Habrink, M., Hammer, E., Völker, U. & Stülke, J. Novel activities of glycolytic enzymes in Bacillus subtilis: Interactions with essential proteins involved in mRNA processing. subm.
+
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]
−
# Doan, T., and S. Aymerich. 2003. Regulation of the central glycolytic pathways in Bacillus subtilis: binding of the repressor CggR to its single DNA target sequence is modulated by fructose-1,6-bisphosphate. Mol. Microbiol. 47: 1709-1721. [http://www.ncbi.nlm.nih.gov/sites/entrez/12622823 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]
−
# Doan et al. (2008) A phospho-sugar binding domain homologous to NagB enzymes regulates the activity of the central glycolytic genes repressor. Proteins 71:2038-2050. [http://www.ncbi.nlm.nih.gov/sites/entrez/18186488 PubMed]
+
# Gao et al. (2002) The E1beta and E2 subunits of the ''Bacillus subtilis'' pyruvate dehydrogenase complex are involved in regulation of sporulation.''J. Bacteriol.'' '''184:''' 2780-2788. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
−
# Fillinger, S., Boschi-Muller, S., Azza, S., Dervyn, E., Branlant, G., and Aymerich, S. (2000) Two glyceraldehyde-3-phosphate dehydrogenases with opposite physiological roles in a nonphotosynthetic bacterium. J Biol Chem 275, 14031-14037. [http://www.ncbi.nlm.nih.gov/sites/entrez/10799476 PubMed]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
−
# Ludwig, H., Homuth, G., Schmalisch, M., Dyka, F. M., Hecker, M., and Stülke, J. (2001) Transcription of glycolytic genes and operons in ''Bacillus subtilis'': evidence for the presence of multiple levels of control of the ''gapA'' operon. Mol Microbiol 41, 409-422.[http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]
 
−
# Ludwig, H., Rebhan, N., Blencke, H.-M., Merzbacher, M. & Stülke, J. (2002). Control of the glycolytic ''gapA'' operon by the catabolite control protein A in ''Bacillus subtilis'': a novel mechanism of CcpA-mediated regulation. Mol Microbiol 45, 543-553.[http://www.ncbi.nlm.nih.gov/sites/entrez/12123463 PubMed]
 
−
# Meinken, C., Blencke, H. M., Ludwig, H., and Stülke, J. (2003) Expression of the glycolytic ''gapA'' operon in ''Bacillus subtilis'': differential synthesis of proteins encoded by the operon. Microbiology 149, 751-761. [http://www.ncbi.nlm.nih.gov/sites/entrez/12634343 PubMed]
 
−
# Rezacova et al. (2008) Crystal structures of the effector-binding domain of repressor Central glycolytic gene Regulator from Bacillus subtilis reveal ligand-induced structural changes upon binding of several glycolytic intermediates. Mol. Microbiol. 69:895-910. [http://www.ncbi.nlm.nih.gov/sites/entrez/18554327 PubMed]
 
−
# Zorilla et al. (2007) Fructose-1,6-bisphosphate acts both as an inducer and as a structural cofactor of the central glycolytic genes repressor (CggR). Biochemistry 46:14996-15008. [http://www.ncbi.nlm.nih.gov/sites/entrez/18052209 PubMed]
 
−
# Zorilla et al. (2007) Inducer-modulated cooperative binding of the tetrameric CggR repressor to operator DNA. Biophys. J. 92: 3215-3227. [http://www.ncbi.nlm.nih.gov/sites/entrez/17293407 PubMed]
 

Revision as of 22:24, 1 April 2009

  • Description: pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit)

Gene name pdhC
Synonyms
Essential no
Product pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit)
Function links glycolysis and TCA cycle
MW, pI 47 kDa, 4.855
Gene length, protein length 1326 bp, 442 aa
Immediate neighbours pdhB, pdhD
Gene sequence (+200bp) Protein sequence
Genetic context
PdhC context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

defects in sporulation and unable to grow on glucose as single carbon source PubMed

Database entries

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

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:
  • Localization: membrane associated PubMed

Database entries

  • Structure: 1W88 (E1 in complex with subunit binding domain of E2, Geobacillus stearothermophilus), 2PDE (peripheral subunit binding domain, Geobacillus stearothermophilus), 1LAC (lipoyl domain, Geobacillus stearothermophilus), 1B5S (catalytic domain (residues 184-425) , Geobacillus stearothermophilus)
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number: 2.3.1.12

Additional information

Expression and regulation

  • Regulation: expression activated by glucose (1.94) PubMed, weak induction by glucose 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

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
  1. Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 8: 4123-4136 PubMed
  2. Gao et al. (2002) The E1beta and E2 subunits of the Bacillus subtilis pyruvate dehydrogenase complex are involved in regulation of sporulation.J. Bacteriol. 184: 2780-2788. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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