Difference between revisions of "Sandbox"

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* '''Description:''' DNA-Gyrase (subunit A) <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'''
−
|''gyrA''
+
|''gyrB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''nalA ''
+
|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-Gyrase (subunit A)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || DNA-Gyrase (subunit B)
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || DNA supercoiling, <br/>initation of replication cycle and DNA elongation
 
|style="background:#ABCDEF;" align="center"|'''Function''' || DNA supercoiling, <br/>initation of replication cycle and DNA elongation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 91 kDa, 5.215  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 71 kDa, 5.378  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2463 bp, 821 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1914 bp, 638 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gyrB]]'', ''[[rrnO-16S]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaB]]'', ''[[gyrA]]''
 
|-
 
|-
 
|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:GyrA_context.png]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:DnaA_dnaN_yaaA_recF_yaaB_gyrB_context.png]]
 
  <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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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gyrA.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+BG10071]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10070]
  
 
=== Additional information===
 
=== Additional information===
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* '''Protein family:'''
 
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[ParC]]
+
* '''Paralogous protein(s):''' [[ParE]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 72: Line 72:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' GyrA-[[GyrB]]
+
* '''Interactions:''' [[GyrA]]-GyrB
  
−
* '''Localization:''' Nucleoid (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed] nucleoid-associated in actively growing cells [http://www.ncbi.nlm.nih.gov/sites/entrez/9539793 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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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00070]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00060]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
−
 
−
:* 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]
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''gyrA'' [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]
Line 100: Line 98:
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:''' 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],  GyrA 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]
+
* '''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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=References=
 
=References=
  
−
# 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]
 
−
# 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]
 
# 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]
 
# 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]

Revision as of 21:44, 15 April 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
Hier soll was neues rein
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:
  • Protein family:
  • Paralogous protein(s): ParE

Extended information on the protein

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

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [3]
  • 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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