Difference between revisions of "Sandbox"

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* '''Description:''' seryl-tRNA synthetase <br/><br/>
+
* '''Description:''' DNA polymerase III (gamma and tau subunits)DNA polymerase III (gamma and tau subunits)<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'''
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|''serS''
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|''dnaX''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dnaH, dna-8132 ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes   
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes   
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || seryl-tRNA synthetase (EC 6.1.1.11)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || DNA polymerase III (gamma and tau subunits) (EC 2.7.7.7)
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' ||  
 
|style="background:#ABCDEF;" align="center"|'''Function''' ||  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 5.193  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 62 kDa, 5.488  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1275 bp, 425 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1689 bp, 563 aa  
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' ||  
 
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' ||  
 
|-
 
|-
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/serS_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/dnaX_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/serS_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/dnaX_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:serS_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:dnaX_context.gif]]
 
|-
 
|-
 
|}
 
|}
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=== Database entries ===
 
=== Database entries ===
  
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* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/serS.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dnaX.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10077]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10083]
  
 
=== Additional information===
 
=== Additional information===
Line 73: Line 73:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[DnaX]]-[[DnaB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/14757052 PubMed]
  
−
* '''Localization:'''
+
* '''Localization:''' nucleoid region (mid-cell spot) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''serS'' [http://www.ncbi.nlm.nih.gov/sites/entrez/8915527 PubMed]
+
* '''Operon:'''  
  
 
* '''Sigma factor:'''  
 
* '''Sigma factor:'''  
  
−
* '''Regulation:''' induced in the presence of serine [http://www.ncbi.nlm.nih.gov/sites/entrez/8915527 PubMed]
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' antitermination by a ''[[trnD-Ser]]-''dependent RNA switch [http://www.ncbi.nlm.nih.gov/sites/entrez/8915527 PubMed]
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
−
# Condon et al. (1996) Aminoacyl-tRNA synthetase gene regulation in ''Bacillus subtilis''.
+
# Haroniti et al. (2004) The clamp-loader-helicase interaction in ''Bacillus''. Atomic force microscopy reveals the structural organisation of the DnaB-tau complex in ''Bacillus''.''J. Mol. Biol.'' '''336:''' 381-393. [http://www.ncbi.nlm.nih.gov/sites/entrez/14757052 PubMed]
−
''Biochimie'' '''78:''' 381-389. [http://www.ncbi.nlm.nih.gov/sites/entrez/8915527 PubMed]
+
# Meile et al. (2006) Systematic localisation of proteins fused to the green fluorescent protein in Bacillus subtilis: identification of new proteins at the DNA replication factory ''Proteomics'' '''6:''' 2135-2146. [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]

Revision as of 12:48, 9 February 2009

  • Description: DNA polymerase III (gamma and tau subunits)DNA polymerase III (gamma and tau subunits)

Gene name dnaX
Synonyms dnaH, dna-8132
Essential yes
Product DNA polymerase III (gamma and tau subunits) (EC 2.7.7.7)
Function
MW, pI 62 kDa, 5.488
Gene length, protein length 1689 bp, 563 aa
Immediate neighbours
Gene sequence (+200bp) Protein sequence
Genetic context
DnaX context.gif



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

essential

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:
  • Localization: nucleoid region (mid-cell spot) PubMed

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry:
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Sigma factor:
  • Regulation:
  • 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. Haroniti et al. (2004) The clamp-loader-helicase interaction in Bacillus. Atomic force microscopy reveals the structural organisation of the DnaB-tau complex in Bacillus.J. Mol. Biol. 336: 381-393. PubMed
  2. Meile et al. (2006) Systematic localisation of proteins fused to the green fluorescent protein in Bacillus subtilis: identification of new proteins at the DNA replication factory Proteomics 6: 2135-2146. PubMed
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