Difference between revisions of "Sandbox"

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* '''Description:''' DNA polymerase  III (beta subunit), beta clamp <br/><br/>
+
* '''Description:''' DNA-Gyrase (subunit B) <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'''
−
|''dnaN''
+
|''gyrB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dnaG, dnaK ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''novA ''
 
|-
 
|-
 
|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''' || DNA polymerase  III <br/>(beta subunit), beta clamp
+
|style="background:#ABCDEF;" align="center"| '''Product''' || DNA-Gyrase (subunit B)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || DNA replication
+
|style="background:#ABCDEF;" align="center"|'''Function''' || DNA supercoiling, <br/>initation of replication cycle and DNA elongation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 41 kDa, 4.718  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 71 kDa, 5.378  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1134 bp, 378 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1914 bp, 638 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dnaA]]'', ''[[yaaA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaB]]'', ''[[gyrA]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11778&#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:CAB11782&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
 
|colspan="2" | '''Genetic context''' <br/> [[Image:DnaA_dnaN_yaaA_recF_yaaB_gyrB_context.png]]
 
|colspan="2" | '''Genetic context''' <br/> [[Image:DnaA_dnaN_yaaA_recF_yaaB_gyrB_context.png]]
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dnaAN.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yaaA-recF-yaaB-gyrB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10066]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10070]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1) (according to Swiss-Prot)  
+
* '''Catalyzed reaction/ biological activity:''' ATP-dependent breakage, passage and rejoining of double-stranded DNA (according to Swiss-Prot)  
  
−
* '''Protein family:'''
+
* '''Protein family:''' type II topoisomerase family (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[ParE]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[DnaA]]-[[YabA]]-[[DnaN]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12060778 PubMed]
+
* '''Interactions:''' [[GyrA]]-[[GyrB]]
  
−
* '''Localization:''' cytoplasm (according to Swiss-Prot),  Nucleoid (Mid-cell) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed] nucleoid (mid-cell spot) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
+
* '''Localization:''' nucleoid-associated in actively growing cells [http://www.ncbi.nlm.nih.gov/sites/entrez/9539793 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P05649 P05649]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P05652 P05652]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00020 BSU00020]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00060 BSU00060]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.7.7 2.7.7.7]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[dnaA]]-[[dnaN]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
+
* '''Operon:''' ''[[yaaA]]-[[recF]]-[[yaaB]]-[[gyrB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
  
−
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
+
* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
  
−
* '''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]
+
* '''Regulation:'''  
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:''' GyrB is subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
  
 
=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]
+
 
 +
[[Dagmar Klostermeier]], Biozentrum Basel, Switzerland [http://www.biozentrum.unibas.ch/klostermeier/index.html homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
# 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]
+
# Huang et al. (1998) Bipolar localization of Bacillus subtilis topoisomerase IV, an enzyme required for chromosome segregation. ''Proc. Natl. Acad. Sci. USA'' '''95:''' 4652-4657. [http://www.ncbi.nlm.nih.gov/sites/entrez/9539793 PubMed]
 +
# Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 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]
 
# 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]
 
−
# 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]
 
−
# 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]
 
−
# 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]
 
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 

Revision as of 09:52, 23 May 2009

  • Description: DNA-Gyrase (subunit B)

Gene name gyrB
Synonyms novA
Essential yes PubMed
Product DNA-Gyrase (subunit B)
Function DNA supercoiling,
initation of replication cycle and DNA elongation
MW, pI 71 kDa, 5.378
Gene length, protein length 1914 bp, 638 aa
Immediate neighbours yaaB, gyrA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
DnaA dnaN yaaA recF yaaB gyrB context.png
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-dependent breakage, passage and rejoining of double-stranded DNA (according to Swiss-Prot)
  • Protein family: type II topoisomerase family (according to Swiss-Prot)
  • Paralogous protein(s): ParE

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Localization: nucleoid-associated in actively growing cells PubMed

Database entries

  • Structure:
  • E.C. number:

Additional information

Expression and regulation

  • Regulation:
  • Regulatory mechanism:
  • Additional information: GyrB is subject to Clp-dependent proteolysis upon glucose starvation PubMed

Biological materials

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

Labs working on this gene/protein

Dagmar Klostermeier, Biozentrum Basel, Switzerland homepage

Your additional remarks

References

  1. Huang et al. (1998) Bipolar localization of Bacillus subtilis topoisomerase IV, an enzyme required for chromosome segregation. Proc. Natl. Acad. Sci. USA 95: 4652-4657. PubMed
  2. Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 PubMed
  3. 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
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