Difference between revisions of "Sandbox"

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−
* '''Description:''' 2-oxoglutarate dehydrogenase complex (dihydrolipoamide transsuccinylase, E2 subunit) <br/><br/>
+
* '''Description:''' general stress protein <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'''
−
|''odhB''
+
|''ohrB ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citM ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yzzE, ykzA ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || 2-oxoglutarate dehydrogenase complex
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
−
(dihydrolipoamide transsuccinylase, E2 subunit)
 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
+
|style="background:#ABCDEF;" align="center"|'''Function''' || organic peroxide resistance
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 45 kDa, 4.859  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 14 kDa, 4.735  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1251 bp, 417 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 408 bp, 136 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[odhA]], [[yocS]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ohrR]]'', ''[[guaD]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13828&#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:CAB13173&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ykzA_context.gif]]
−
|-
 
−
|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>
 
|-
 
|-
Line 32: Line 29:
 
__TOC__
 
__TOC__
  
−
<br/><br/><br/><br/><br/><br/>
+
<br/><br/>
  
 
=The gene=
 
=The gene=
Line 38: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU19360
+
* '''Locus tag:''' BSU13160
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/odhAB.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ohrB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10273]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG19021]
  
 
=== Additional information===
 
=== Additional information===
Line 57: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' Succinyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-succinyldihydrolipoyl)lysine (according to Swiss-Prot)
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' sodium:bile acid symporter family (according to Swiss-Prot)
+
* '''Protein family:''' osmC/ohr family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[OdhA]]-[[OdhB]]-[[PdhD]]
+
* '''Interactions:'''
  
−
* '''Localization:''' cell membrane (according to Swiss-Prot),  membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2BJO 2BJO]
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P16263 P16263]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P80242 P80242]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU19360]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU13160]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.3.1.61 2.3.1.61] 1
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
  
 +
:* subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[odhA]]''-''[[odhB]]''
+
* '''Operon:'''  
  
−
* '''Sigma factor:''' [[SigA]]
+
* '''[[Sigma factor]]:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]  
  
−
* '''Regulation:''' repressed by glucose (2.4-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  constitutive
+
* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
  
−
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
−
<pubmed>12850135 18763711 12682299, </pubmed>
+
<pubmed>15805528, </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]
+
# H&ouml;per et al. (2005) Comprehensive Characterization of the Contribution of Individual [[SigB]]-Dependent General Stress Genes to Stress Resistance of ''Bacillus subtilis''. J. Bact. '''187:''' 2810-2826  [http://www.ncbi.nlm.nih.gov/pubmed/15805528 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]
+
# Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 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]
 
 
# 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 13:27, 8 June 2009

  • Description: general stress protein

Gene name ohrB
Synonyms yzzE, ykzA
Essential no
Product unknown
Function organic peroxide resistance
MW, pI 14 kDa, 4.735
Gene length, protein length 408 bp, 136 aa
Immediate neighbours ohrR, guaD
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YkzA context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU13160

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: osmC/ohr family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • KEGG entry: [3]
  • E.C. number:

Additional information

  • subject to Clp-dependent proteolysis upon glucose starvation PubMed

Expression and regulation

  • Operon:
  • Regulatory mechanism:
  • Additional information: subject to Clp-dependent proteolysis upon glucose starvation PubMed

Biological materials

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

Labs working on this gene/protein

Your additional remarks

References

Dirk Höper, Uwe Völker, Michael Hecker
Comprehensive characterization of the contribution of individual SigB-dependent general stress genes to stress resistance of Bacillus subtilis.
J Bacteriol: 2005, 187(8);2810-26
[PubMed:15805528] [WorldCat.org] [DOI] (P p)

  1. Höper et al. (2005) Comprehensive Characterization of the Contribution of Individual SigB-Dependent General Stress Genes to Stress Resistance of Bacillus subtilis. J. Bact. 187: 2810-2826 PubMed
  2. Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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