Difference between revisions of "Sandbox"

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* '''Description:''' DNA-Gyrase (subunit B) <br/><br/>
+
* '''Description:''' DNA-Gyrase (subunit A) <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'''
−
|''gyrB''
+
|''gyrA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''novA ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''nalA ''
 
|-
 
|-
 
|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 B)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || DNA-Gyrase (subunit A)
 
|-
 
|-
 
|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''' || 71 kDa, 5.378  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 91 kDa, 5.215  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1914 bp, 638 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2463 bp, 821 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[remB]]'', ''[[gyrA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gyrB]]'', ''[[rrnO-16S]]''
 
|-
 
|-
−
|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" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11783&#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:GyrA_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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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU00060
+
* '''Locus tag:''' BSU00070
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yaaA-recF-yaaB-gyrB.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gyrA.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10070]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10071]
  
 
=== Additional information===
 
=== Additional information===
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* '''Catalyzed reaction/ biological activity:''' ATP-dependent breakage, passage and rejoining of double-stranded DNA (according to Swiss-Prot)  
 
* '''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)
+
* '''Protein family:''' topoisomerase gyrA/parC subunit family (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):''' [[ParE]]
+
* '''Paralogous protein(s):''' [[ParC]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Interactions:''' [[GyrA]]-[[GyrB]]
 
* '''Interactions:''' [[GyrA]]-[[GyrB]]
  
−
* '''Localization:''' nucleoid-associated in actively growing cells [http://www.ncbi.nlm.nih.gov/sites/entrez/9539793 PubMed]
+
* '''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]
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P05652 P05652]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P05653 P05653]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00060]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00070]
  
 
* '''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:''' ''[[yaaA]]-[[recF]]-[[yaaB]]-[[gyrB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
+
* '''Operon:''' ''gyrA'' [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]
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* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''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]
+
* '''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]
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
−
<pubmed>17981983 ,9539793 , 2987848  </pubmed>
+
<pubmed>16479537,17981983 ,9539793 , 2987848  </pubmed>

Revision as of 12:47, 14 June 2009

  • Description: DNA-Gyrase (subunit A)

Gene name gyrA
Synonyms nalA
Essential yes PubMed
Product DNA-Gyrase (subunit A)
Function DNA supercoiling,
initation of replication cycle and DNA elongation
MW, pI 91 kDa, 5.215
Gene length, protein length 2463 bp, 821 aa
Immediate neighbours gyrB, rrnO-16S
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
GyrA context.png
This image was kindly provided by SubtiList




The gene

Basic information

  • Locus tag: BSU00070

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: topoisomerase gyrA/parC subunit family (according to Swiss-Prot)
  • Paralogous protein(s): ParC

Extended information on the protein

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

Database entries

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

Additional information

  • subject to Clp-dependent proteolysis upon glucose starvation PubMed

Expression and regulation

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

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