Difference between revisions of "Sandbox"

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* '''Description:''' dihydrolipoamide dehydrogenase E3 subunit of both pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase complexes  <br/><br/>
+
* '''Description:''' acetate kinase <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'''
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|''pdhD''
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|''ackA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citL ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || dihydrolipoamide dehydrogenase E3 subunit<br/> of both pyruvate dehydrogenase and 2-oxoglutarate<br/> dehydrogenase complexes
+
|style="background:#ABCDEF;" align="center"| '''Product''' || acetate kinase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || links glycolysis and TCA cycle, enzyme in TCA cycle
+
|style="background:#ABCDEF;" align="center"|'''Function''' || overflow metabolism
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 49 kDa, 4.76  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 42 kDa, 5.191  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1410 bp, 470 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1185 bp, 395 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pdhC]]'', ''[[slp]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[moaB]]'', ''[[ytxK]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pdhD_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ackA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/pdhD_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ackA_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:pdhD_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ackA_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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__TOC__
 
__TOC__
  
−
<br/><br/><br/><br/>
+
<br/><br/>
  
 
=The gene=
 
=The gene=
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===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/pdhABCD.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ackA.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10210]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10813]
  
 
=== Additional information===
 
=== Additional information===
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[PdhA]]-[[PdhB]]-[[PdhC]]-[[PdhD]], [[OdhA]]-[[OdhB]]-[[PdhD]]
+
* '''Interactions:'''
  
 
* '''Localization:'''
 
* '''Localization:'''
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=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1EBD 1EBD] (complex with binding domain of dihydrolipoamide acetylase, ''Geobacillus stearothermophilus'')
+
* '''Structure:'''
  
−
* '''Swiss prot entry:'''  
+
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14610]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29470]
  
−
* '''E.C. number:''' 1.8.1.4
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[pdhA]]-[[pdhB]]-[[pdhC]]-[[pdhD]]''
+
* '''Operon:'''  
  
−
* '''Sigma factor:''' [[SigA]]
+
* '''Sigma factor:'''  
  
−
* '''Regulation:''' expression activated by glucose (2.03) [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 (2.46) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]   
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
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=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=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 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 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]
−
# 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]
+
# Grundy FJ, Waters DA, Allen SH, Henkin TM (1993) Regulation of the Bacillus subtilis acetate kinase gene by CcpA. J Bacteriol 175:7348-7355 [http://www.ncbi.nlm.nih.gov/sites/entrez/8226682 PubMed]
 +
# Turinsky, A. J., Grundy, F. J., Kim, J. H., Chambliss, G. H., and Henkin, T. M. 1998. Transcriptional activation of the Bacillus subtilis ackA gene requires sequences upstream of the promoter. J. Bacteriol. 180: 5961-5967. [http://www.ncbi.nlm.nih.gov/sites/entrez/9811655 PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 22:26, 1 April 2009

  • Description: acetate kinase

Gene name ackA
Synonyms
Essential no
Product acetate kinase
Function overflow metabolism
MW, pI 42 kDa, 5.191
Gene length, protein length 1185 bp, 395 aa
Immediate neighbours moaB, ytxK
Gene sequence (+200bp) Protein sequence
Genetic context
AckA context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

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:
  • Interactions:
  • Localization:

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Sigma factor:
  • Regulation: expression activated by glucose (2.46) PubMed
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Linc Sonenshein, Tufts University, Boston, MA, USA Homepage

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. Grundy FJ, Waters DA, Allen SH, Henkin TM (1993) Regulation of the Bacillus subtilis acetate kinase gene by CcpA. J Bacteriol 175:7348-7355 PubMed
  3. Turinsky, A. J., Grundy, F. J., Kim, J. H., Chambliss, G. H., and Henkin, T. M. 1998. Transcriptional activation of the Bacillus subtilis ackA gene requires sequences upstream of the promoter. J. Bacteriol. 180: 5961-5967. PubMed
  4. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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