Difference between revisions of "Sandbox"

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* '''Description:''' isocitrate dehydrogenase <br/><br/>
+
* '''Description:''' 2-oxoglutarate dehydrogenase complex (dihydrolipoamide transsuccinylase, 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'''
−
|''icd''
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|''odhB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citC ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citM ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || isocitrate dehydrogenase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || 2-oxoglutarate dehydrogenase complex
 +
(dihydrolipoamide transsuccinylase, E2 subunit)
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle  
 
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46 kDa, 4.833  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 45 kDa, 4.859  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1269 bp, 423 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1251 bp, 417 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[citZ]], [[mdh]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[odhA]], [[yocS]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/icd_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/odhB_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/icd_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/odhB_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:icd_context.gif]]
+
|colspan="2" style="background:#FAF8CC;color:#FF0000" align="center" | '''Caution: The sequence for this gene in SubtiList contains errors
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:odhB_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/><br/><br/>
  
 
=The gene=
 
=The gene=
Line 39: Line 42:
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
reduced ability to sporulate [http://www.ncbi.nlm.nih.gov/pubmed/9244258 PubMed]
+
 
 +
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/odhAB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10856]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10273]
  
 
=== Additional information===
 
=== Additional information===
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylated [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' attached to the membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
+
* '''Localization:''' membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1HQS 1HQS]
+
* '''Structure:'''
  
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29130]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU19360]
  
−
* '''E.C. number:''' 1.1.1.42
+
* '''E.C. number:''' 2.3.1.61
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[odhA]]''-''[[odhB]]''
−
**''[[citZ]]-[[icd]]-[[mdh]]''
 
−
**''[[icd]]-[[mdh]]''
 
  
 
* '''Sigma factor:''' [[SigA]]
 
* '''Sigma factor:''' [[SigA]]
  
−
* '''Regulation:''' repressed by glucose (2.2-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  ''[[citZ]]'': catabolite repression ([[CcpA]]), repression by glucose + glutamate ([[CcpC]])
+
* '''Regulation:''' repressed by glucose (2.4-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  constitutive
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''[[icd]]'': constitutive
+
 
−
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression,  [[CcpA]]: transcription repression
+
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression  
  
 
* '''Additional information:'''
 
* '''Additional information:'''
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=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP666 (spc), GP672 (erm), available in [[Stülke]] lab
+
* '''Mutant:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
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# 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]
−
# Matsuno K, Blais T, Serio AW, Conway T, Henkin TM, Sonenshein AL (1999) Metabolic imbalance and sporulation in an isocitrate dehydrogenase mutant of Bacillus subtilis. J Bacteriol 181:3382-3391. [http://www.ncbi.nlm.nih.gov/sites/entrez/10348849 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]# Kobayashi et al. (2003) Essential ''Bacillus subtilis'' genes. Proc. Natl. Acad. Sci. USA 100: 4678-4683. [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
−
# Singh SK, Miller SP, Dean A, Banaszak LJ, LaPorte DC (2002) Bacillus subtilis isocitrate dehydrogenase. A substrate analogue for Escherichia coli isocitrate dehydrogenase kinase/ phosphatase. J Biol Chem 277: 7567-7573. [http://www.ncbi.nlm.nih.gov/sites/entrez/11751849 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]
 
# 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]
−
# Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in ''Bacillus subtilis''. Proteomics 7: 3509-3526. [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
 
−
# Levine et al. (2006) Analysis of the dynamic ''Bacillus subtilis'' Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. Proteomics 6, 2157-2173. [http://www.ncbi.nlm.nih.gov/pubmed/16493705 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 10:00, 6 April 2009

  • Description: 2-oxoglutarate dehydrogenase complex (dihydrolipoamide transsuccinylase, E2 subunit)

Gene name odhB
Synonyms citM
Essential yes PubMed
Product 2-oxoglutarate dehydrogenase complex

(dihydrolipoamide transsuccinylase, E2 subunit)

Function TCA cycle
MW, pI 45 kDa, 4.859
Gene length, protein length 1251 bp, 417 aa
Immediate neighbours odhA, yocS
Gene sequence (+200bp) Protein sequence
Caution: The sequence for this gene in SubtiList contains errors
Genetic context
OdhB context.gif
This image was kindly provided by SubtiList







The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

essential 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:
  • Interactions:
  • Localization: membrane associated PubMed

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number: 2.3.1.61

Additional information

Expression and regulation

  • Regulation: repressed by glucose (2.4-fold) (CcpA) PubMed, constitutive
  • Regulatory mechanism: CcpA: transcription repression
  • 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

  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. Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 8: 4123-4136 PubMed# Kobayashi et al. (2003) Essential Bacillus subtilis genes. Proc. Natl. Acad. Sci. USA 100: 4678-4683. PubMed
  3. Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 8: 4123-4136 PubMed
  4. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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