Difference between revisions of "Sandbox"

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−
* '''Description:''' penicillin-binding protein 5*, D-alanyl-D-alanine carboxypeptidase <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'''
−
|''dacA''
+
|''serS''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|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''' || penicillin-binding protein 5*, <br/>D-alanyl-D-alanine carboxypeptidase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || seryl-tRNA-synthetase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || carboxypeptidase
+
|style="background:#ABCDEF;" align="center"|'''Function''' || translation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 5.668  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 5.193  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1329 bp, 443 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1275 bp, 425 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[guaB]]'', ''[[pdxS]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pdxT]]'', ''[[trnSL-Ser1]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11786&#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:dacA_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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__TOC__
 
__TOC__
  
−
<br/><br/><br/>
+
<br/><br/>
  
 
=The gene=
 
=The gene=
Line 38: Line 38:
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/serS.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10074]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10077]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala (according to Swiss-Prot)  
+
* '''Catalyzed reaction/ biological activity:''' ATP + L-serine + tRNA(Ser) = AMP + diphosphate + L-seryl-tRNA(Ser) (according to Swiss-Prot)  
  
−
* '''Protein family:''' peptidase S11 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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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' secreted (according to Swiss-Prot),  membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
+
* '''Localization:''' cytoplasm (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P08750 P08750]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P37464 P37464]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00100 BSU00100]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00130 BSU00130]
  
−
* '''E.C. number:'''
+
* '''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=
  
−
* '''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=
  
−
# 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]
+
# Condon et al. (1996) Aminoacyl-tRNA synthetase gene regulation in ''Bacillus subtilis''.
 +
''Biochimie'' '''78:''' 381-389. [http://www.ncbi.nlm.nih.gov/sites/entrez/8915527 PubMed]

Revision as of 10:57, 23 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: ATP + L-serine + tRNA(Ser) = AMP + diphosphate + L-seryl-tRNA(Ser) (according to Swiss-Prot)
  • 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:

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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