Difference between revisions of "Sandbox"

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−
* '''Description:''' write here <br/><br/>
+
* '''Description:''' replication initiation 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'''
−
|''thiL''
+
|''dnaA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ydiA, ydxA ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dnaH, dnaJ, dnaK ''
 
|-
 
|-
−
|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''' || thiamine-monophosphate kinase (EC 2.7.4.16)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || replication initiation protein
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' ||  
+
|style="background:#ABCDEF;" align="center"|'''Function''' || DNA replication
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 35 kDa, 5.036  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 6.035  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 975 bp, 325 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1338 bp, 446 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[trnE-Asp]]'', ''[[ydiB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rpmH]]'', ''[[dnaN]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/thiL_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/dnaA_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/thiL_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/dnaA_protein.txt Protein sequence]'''
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:thiL_context.gif]]
 
 
|-
 
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:dnaA_context.gif]]
 +
<div align="right"> <small>the origin of the image is [http://genolist.pasteur.fr/SubtiList/ SubtiList]<small>|-
 
|}
 
|}
  
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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:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dnaAN.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10693]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10065]
  
 
=== Additional information===
 
=== Additional information===
Line 60: Line 62:
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
  
−
* '''Kinetic information:''' information:
+
* '''Kinetic information:'''
  
 
* '''Domains:'''  
 
* '''Domains:'''  
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[DnaA]]-[[YabA]]-[[DnaN]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12060778 PubMed], [[DnaA]]-[[DnaD]] [http://www.ncbi.nlm.nih.gov/sites/entrez/11222620 PubMed]
  
−
* '''Localization:'''
+
* '''Localization:''' throughout the cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/10844689 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU05900]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00010]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[dnaA]]-[[dnaN]]''  [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
  
−
* '''Sigma factor:'''  
+
* '''Sigma factor:''' [[SigA]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' negatively controlled by [[DnaA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2168872 PubMed] and [[Spo0A]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
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=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
[[Philippe Noirot]], Jouy-en-Josas, France [http://locus.jouy.inra.fr/cms/index.php?id=18 homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 118: Line 121:
 
=References=
 
=References=
  
 +
# Imai et al. (2000) Subcellular localization of Dna-initiation proteins of ''Bacillus subtilis'': evidence that chromosome replication begins at either edge of the nucleoids. ''Mol. Microbiol.'' '''36:''' 1037-1048. [http://www.ncbi.nlm.nih.gov/sites/entrez/10844689 PubMed]
 +
# Ishigo-Oka et al. (2001) DnaD protein of ''Bacillus subtilis'' interacts with DnaA, the initiator protein of replication. ''J. Bacteriol.'' '''183:''' 2148-2150. [http://www.ncbi.nlm.nih.gov/sites/entrez/11222620 PubMed]
 +
# Noirot-Gros et al. (2002) An expanded view of bacterial DNA replication. ''Proc. Natl. Acad. Sci. USA'' '''99:''' 8342-8347. [http://www.ncbi.nlm.nih.gov/sites/entrez/12060778 PubMed]
 +
# Noirot-Gros et al. (2002) Functional dissection of YabA, a negative regulator of DNA replication initiation in Bacillus Title ''Proc. Natl. Acad. Sci. USA'' '''103:''' 2368-2373. [http://www.ncbi.nlm.nih.gov/sites/entrez/16461910 PubMed]
 +
# Ogasawara et al. (1985) Structure and function of the region of the replication origin of the ''Bacillus subtilis'' chromosome. IV. Transcription of the oriC region and expression of DNA gyrase genes and other open reading frames.''Nucl. Acids Res.'' '''11:''' 2267-2279. [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
 +
# Fukuoka et al.  (1990) Purification and characterization of an initiation protein for chromosomal replication, DnaA, in ''Bacillus subtilis''. ''J. Biochem.'' '''107:''' 732-739. [http://www.ncbi.nlm.nih.gov/sites/entrez/2168872 PubMed]
 +
# Molle et al. (2003) The Spo0A regulon of ''Bacillus subtilis''.''Mol. Microbiol.'' '''50:''' 1683-1701. [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 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 14:59, 20 March 2009

  • Description: replication initiation protein

Gene name dnaA
Synonyms dnaH, dnaJ, dnaK
Essential yes PubMed
Product replication initiation protein
Function DNA replication
MW, pI 50 kDa, 6.035
Gene length, protein length 1338 bp, 446 aa
Immediate neighbours rpmH, dnaN
Gene sequence (+200bp) Protein sequence
Genetic context
DnaA context.gif
the origin of the image is 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:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Localization: throughout the cytoplasm PubMed

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulatory mechanism:
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Philippe Noirot, Jouy-en-Josas, France homepage

Your additional remarks

References

  1. Imai et al. (2000) Subcellular localization of Dna-initiation proteins of Bacillus subtilis: evidence that chromosome replication begins at either edge of the nucleoids. Mol. Microbiol. 36: 1037-1048. PubMed
  2. Ishigo-Oka et al. (2001) DnaD protein of Bacillus subtilis interacts with DnaA, the initiator protein of replication. J. Bacteriol. 183: 2148-2150. PubMed
  3. Noirot-Gros et al. (2002) An expanded view of bacterial DNA replication. Proc. Natl. Acad. Sci. USA 99: 8342-8347. PubMed
  4. Noirot-Gros et al. (2002) Functional dissection of YabA, a negative regulator of DNA replication initiation in Bacillus Title Proc. Natl. Acad. Sci. USA 103: 2368-2373. PubMed
  5. Ogasawara et al. (1985) Structure and function of the region of the replication origin of the Bacillus subtilis chromosome. IV. Transcription of the oriC region and expression of DNA gyrase genes and other open reading frames.Nucl. Acids Res. 11: 2267-2279. PubMed
  6. Fukuoka et al. (1990) Purification and characterization of an initiation protein for chromosomal replication, DnaA, in Bacillus subtilis. J. Biochem. 107: 732-739. PubMed
  7. Molle et al. (2003) The Spo0A regulon of Bacillus subtilis.Mol. Microbiol. 50: 1683-1701. PubMed
  8. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed

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