Difference between revisions of "Sandbox"

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* '''Description:''' involved in the activation of biofilm matrix biosynthetic operons, acts in parallel to SinR, AbrB, and DegU <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'''
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|''remB''
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|''gyrB''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yaaB''
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''novA ''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || regulator of the extracellular matrix
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|style="background:#ABCDEF;" align="center"| '''Product''' || DNA-Gyrase (subunit B)
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of biofilm formation
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|style="background:#ABCDEF;" align="center"|'''Function''' || DNA supercoiling, <br/>initation of replication cycle and DNA elongation
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 5 kDa, 8.796  
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 71 kDa, 5.378  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 156 bp, 52 aa  
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1914 bp, 638 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[recF]]'', ''[[gyrB]]''
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[remB]]'', ''[[gyrA]]''
 
|-
 
|-
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|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11781&#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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__TOC__
 
__TOC__
  
−
<br/><br/>
+
<br/><br/><br/>
  
 
=The gene=
 
=The gene=
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU00050
+
* '''Locus tag:''' BSU00060
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
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* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yaaA-recF-yaaB-gyrB.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+BG10069]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10070]
  
 
=== Additional information===
 
=== Additional information===
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''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:'''
+
* '''Interactions:''' [[GyrA]]-[[GyrB]]
  
−
* '''Localization:'''
+
* '''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/P37525 P37525]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P05652 P05652]
  
−
* '''KEGG entry:''']
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00060]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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* '''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=
 +
 +
[[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=
  
−
<pubmed>,19363116, 19363116, 2987848 </pubmed>
+
<pubmed>17981983 ,9539793 , 2987848 </pubmed>

Revision as of 12:46, 14 June 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 remB, 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

  • Locus tag: BSU00060

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:
  • 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

Ulf Gerth, Holger Kock, Ilja Kusters, Stephan Michalik, Robert L Switzer, Michael Hecker
Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis.
J Bacteriol: 2008, 190(1);321-31
[PubMed:17981983] [WorldCat.org] [DOI] (I p)

W M Huang, J L Libbey, P van der Hoeven, S X Yu
Bipolar localization of Bacillus subtilis topoisomerase IV, an enzyme required for chromosome segregation.
Proc Natl Acad Sci U S A: 1998, 95(8);4652-7
[PubMed:9539793] [WorldCat.org] [DOI] (P p)

N Ogasawara, S Moriya, H Yoshikawa
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.
Nucleic Acids Res: 1985, 13(7);2267-79
[PubMed:2987848] [WorldCat.org] [DOI] (P p)

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