Difference between revisions of "Sandbox"

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−
* '''Description:''' glyceraldehyde-3-phosphate dehydrogenase, NADP-dependent, gluconeogenic enzyme<br/><br/>
+
* '''Description:''' initiation of chromosome replication/ membrane attachment 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'''
−
|''gapB''
+
|''dnaB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ppc''
+
|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''' || glyceraldehyde-3-phosphate dehydrogenase 2
+
|style="background:#ABCDEF;" align="center"| '''Product''' || initiation of chromosome replication/ membrane attachment protein
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || anabolic enzyme in gluconeogenesis
+
|style="background:#ABCDEF;" align="center"|'''Function''' || DNA replication
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 37,3 kDa, 6.47
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 54 kDa, 5.278 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1020 bp, 340 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1416 bp, 472 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytcD]]'', ''[[speD]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dnaI]]'', ''[[ytcG]]''
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:gapB_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:dnaB_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>
 
|-
 
|-
Line 35: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:''' 2966075 - 2967094
+
* '''Coordinates:'''
  
 
===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/gapB-speD.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12592]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10358]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=The protein=
 
=The protein=
Line 51: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' D-glyceraldehyde 3-phosphate + phosphate + NAD(P)(+) = 3-phospho-D-glyceroyl phosphate + NAD(P)H.
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' glyceraldehyde-3-phosphate dehydrogenase family
+
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[GapA]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 62: Line 65:
  
 
* '''Domains:'''  
 
* '''Domains:'''  
−
** Nucleotid bindinge domain (12-13)
 
−
** 2x Glyceraldehyde 3-phosphate binding domain (151-153) & (210-211)
 
  
 
* '''Modification:'''
 
* '''Modification:'''
Line 71: Line 72:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[DnaX]]-[[DnaB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/14757052 PubMed]
  
−
* '''Localization:''' Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
+
* '''Localization:''' Membrane-proximal (Spotty) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed] forms foci, close to oriC [http://www.ncbi.nlm.nih.gov/sites/entrez/10844689 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
Line 79: Line 80:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O34425]
+
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29020]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28990]
  
−
* '''E.C. number:''' [http://www.expasy.ch/cgi-bin/get-enzyme-entry?1.2.1.12 1.2.1.12]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[gapB]]-[[speD]]''
+
* '''Operon:'''  
  
−
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+15720552 PubMed]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' repressed (70-times) by Glc, repressor [[CcpN]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+15720552 PubMed]
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' transcription repression
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 105: Line 105:
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
−
+
       
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
 +
 +
* '''two-hybrid system:'''
  
 
* '''Antibody:'''
 
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 120: Line 120:
 
=References=
 
=References=
  
−
# Fillinger, S., Boschi-Muller, S., Azza, S., Dervyn, E., Branlant, G., and Aymerich, S. (2000) Two glyceraldehyde-3-phosphate dehydrogenases with opposite physiological roles in a nonphotosynthetic bacterium. J Biol Chem 275, 14031-14037. [http://www.ncbi.nlm.nih.gov/sites/entrez/10799476 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]
 
# 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]
−
# Servant et al. (2005) CcpN (YqzB), a novel regulator for CcpA-independent catabolite repression of ''Bacillus subtilis'' gluconeogenic genes. Mol. Microbiol. 55: 1435-1451. [http://www.ncbi.nlm.nih.gov/sites/entrez/15720552 PubMed]
+
# 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]
−
# Tännler et al. (2008) CcpN controls central carbon fluxes in ''Bacillus subtilis''. J. Bacteriol. 190: 6178-6187. [http://www.ncbi.nlm.nih.gov/sites/entrez/18586936 PubMed]
+
# 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]
−
# Thomaides, H. B., Davison, E. J., Burston, L., Johnson, H., Brown, D. R., Hunt, A. C., Errington, J., and Czaplewski, L. (2007) Essential bacterial functions encoded by gene pairs. J Bacteriol 189: 591-602. [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 PubMed]
 

Revision as of 17:20, 15 April 2009

  • Description: initiation of chromosome replication/ membrane attachment protein

Gene name dnaB
Synonyms
Essential yes PubMed
Product initiation of chromosome replication/ membrane attachment protein
Function DNA replication
MW, pI 54 kDa, 5.278
Gene length, protein length 1416 bp, 472 aa
Immediate neighbours dnaI, ytcG
Hier soll was neues rein
Genetic context
DnaB context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

essential PubMed

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

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: Membrane-proximal (Spotty) PubMed forms foci, close to oriC PubMed

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • 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. 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
  2. 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
  3. 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
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