Difference between revisions of "Sandbox"

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* '''Description:''' assembly of the 50S subunit of the ribosome <br/><br/>
+
* '''Description:''' succinate dehydrogenase <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'''
−
|''ysxC''
+
|''sdhB''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|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''' || GTPase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || succinate dehydrogenase (iron-sulfur protein)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || assembly of the 50S subunit of the ribosome
+
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 21 kDa, 9.708  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 7.989  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 585 bp, 195 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 759 bp, 253 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ysxD]]'', ''[[lonA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sdhA]], [[ysmA]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14779&#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:CAB14803&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ysxC_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:sdhB_context.gif]]
 +
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
|-
 
|-
 
|}
 
|}
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===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/lonA-ysxC.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sdhCAB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10339]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10353]
  
 
=== Additional information===
 
=== Additional information===
Line 53: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' Binds and hydrolyzes GTP and readily exchanges GDP for GTP
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' Era/Obg family
+
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[Era]], [[Obg]], [[YphC]], [[YsxC]], [[RbgA]], [[YqeH]], [[ThdF]], [[YyaF]], [[YnbA]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[YsxC]]-[[RplL]],  
+
* '''Interactions:''' [[SdhA]]-[[SdhB]]-[[SdhC]],  
  
−
* '''Localization:'''
+
* '''Localization:''' attached to the membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1NEK 1NEK] (''E. coli'')
  
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28190]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28430]
  
−
* '''E.C. number:'''
+
* '''E.C. number:'''EC 1.3.99.1
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[sdhC]]''-''[[sdhA]]''-''[[sdhB]]''
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigA]]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' constitutive
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 114: Line 113:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Naotake Ogasawara]], Nara, Japan
 
  
 
=Your additional remarks=
 
=Your additional remarks=
  
 
=References=
 
=References=
−
 
+
# 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]
−
# Morimoto T, Loh PC, Hirai T, Asai K, Kobayashi K, Moriya S, Ogasawara N (2002) Six GTP-binding proteins of the Era/Obg family are essential for cell growth in ''Bacillus subtilis''. ''Microbiology'' '''148:''' 3539-3552. [http://www.ncbi.nlm.nih.gov/sites/entrez/12427945 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 00:16, 28 April 2009

  • Description: succinate dehydrogenase

Gene name sdhB
Synonyms
Essential no
Product succinate dehydrogenase (iron-sulfur protein)
Function TCA cycle
MW, pI 28 kDa, 7.989
Gene length, protein length 759 bp, 253 aa
Immediate neighbours sdhA, ysmA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
SdhB 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:
  • Localization: attached to the membrane PubMed

Database entries

  • Structure: 1NEK (E. coli)
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number:EC 1.3.99.1

Additional information

Expression and regulation

  • Regulation: constitutive
  • 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

  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. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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