Difference between revisions of "Sandbox"

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* '''Description:''' IMP dehydrogenase <br/><br/>
+
* '''Description:''' seryl-tRNA-synthetase <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'''
−
|''guaB''
+
|''serS''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''guaA ''
+
|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''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || IMP dehydrogenase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || seryl-tRNA-synthetase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || biosynthesis of GMP
+
|style="background:#ABCDEF;" align="center"|'''Function''' || translation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 6.168  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 5.193  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1464 bp, 488 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1275 bp, 425 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaC]]'', ''[[dacA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pdxT]]'', ''[[trnSL-Ser1]]''
 
|-
 
|-
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|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11785&#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:CAB11789&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:guaB_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:serS_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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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/guaB.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/serS.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10073]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10077]
  
 
=== Additional information===
 
=== Additional information===
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* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' IMPDH/GMPR family (according to Swiss-Prot)
+
* '''Protein family:''' Type-1 seryl-tRNA synthetase subfamily (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylated (STY) [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed], S-cysteinlyation after diamide stress (Cys-308) [http://www.ncbi.nlm.nih.gov/pubmed/17611193 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' cytoplasm (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P21879 P21879]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P37464 P37464]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00090]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00130]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.205 1.1.1.205]
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/6.1.1.11 6.1.1.11]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
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* '''Operon:'''  
+
* '''Operon:''' ''serS'' [http://www.ncbi.nlm.nih.gov/sites/entrez/8915527 PubMed]
  
 
* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:'''  
+
* '''Regulation:''' induced in the presence of serine [http://www.ncbi.nlm.nih.gov/sites/entrez/8915527 PubMed]
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' antitermination by a ''[[trnD-Ser]]-''dependent RNA switch [http://www.ncbi.nlm.nih.gov/sites/entrez/8915527 PubMed]
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
−
# 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]
+
# Condon et al. (1996) Aminoacyl-tRNA synthetase gene regulation in ''Bacillus subtilis''.
−
# 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]
+
''Biochimie'' '''78:''' 381-389. [http://www.ncbi.nlm.nih.gov/sites/entrez/8915527 PubMed]
−
# Hochgräfe et al. (2007) S-cysteinylation is a general mechanism for thiol protection of Bacillus subtilis proteins after oxidative stress. ''J. Biol. Chem.'' 282: 25981-25985. [http://www.ncbi.nlm.nih.gov/pubmed/17611193 PubMed]
 

Revision as of 15:07, 12 May 2009

  • Description: seryl-tRNA-synthetase

Gene name serS
Synonyms
Essential yes PubMed
Product seryl-tRNA-synthetase
Function translation
MW, pI 48 kDa, 5.193
Gene length, protein length 1275 bp, 425 aa
Immediate neighbours pdxT, trnSL-Ser1
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
SerS 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: Type-1 seryl-tRNA synthetase subfamily (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: cytoplasm (according to Swiss-Prot)

Database entries

  • Structure:
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Regulation: induced in the presence of serine PubMed
  • Regulatory mechanism: antitermination by a trnD-Ser-dependent RNA switch PubMed
  • 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. Condon et al. (1996) Aminoacyl-tRNA synthetase gene regulation in Bacillus subtilis.

Biochimie 78: 381-389. PubMed

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