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
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00060 GyrB]
+
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00070 GyrA]
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=GyrB GyrB]
+
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=GyrA GyrA]
 
|-
 
|-
−
|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''' || ''[[yaaB]]'', ''[[gyrA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gyrB]]'', ''[[rrnO-16S]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00060 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00060 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00060 DNA_with_flanks]
+
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00070 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00070 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00070 DNA_with_flanks]
 
|-
 
|-
−
|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>
 
|-
 
|-
−
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=gyrB_4867_6783_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:gyrB_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00060]]
+
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=gyrA_6994_9459_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:gyrA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00070]]
 
|-
 
|-
 
|}
 
|}
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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===
Line 72: Line 72:
 
* '''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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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylated on Ser-400 {{PubMed|20509597}}
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
Line 92: Line 92:
  
 
* '''[[Localization]]:'''  
 
* '''[[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]
 
** nucleoid-associated in actively growing cells [http://www.ncbi.nlm.nih.gov/sites/entrez/9539793 PubMed]
  
Line 97: Line 98:
  
 
* '''Structure:'''
 
* '''Structure:'''
 +
** [http://www.rcsb.org/pdb/explore/explore.do?structureId=4DDQ 4DDQ] (DNA gyrase A-subunit lacking the C-terminal DNA-wrapping domains) {{PubMed|23602808}}
  
−
* '''UniProt:''' [http://www.uniprot.org/uniprot/P05652 P05652]
+
* '''UniProt:''' [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 {{PubMed|17981983}}
  
 
=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]
  
−
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=gyrB_4867_6783_1 gyrB] {{PubMed|22383849}}
+
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=gyrA_6994_9459_1 gyrA] {{PubMed|22383849}}
  
 
* '''[[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 118: Line 122:
 
* '''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 =
Line 141: Line 145:
  
 
=References=
 
=References=
−
'''Additional references:''' {{PubMed|20870749}}
+
<pubmed>16479537,17981983 ,9539793 , 2987848 19666507 17320901 23475963 23602808 20870749</pubmed>
−
<pubmed>17981983 ,9539793 , 2987848 19666507 17320901 20509597 23475963</pubmed>
 
  
 
[[Category:Protein-coding genes]]
 
[[Category:Protein-coding genes]]

Revision as of 14:54, 11 November 2013

  • 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
Gene expression levels in SubtiExpress: GyrA
Interactions involving this protein in SubtInteract: GyrA
MW, pI 91 kDa, 5.215
Gene length, protein length 2463 bp, 821 aa
Immediate neighbours gyrB, rrnO-16S
Sequences Protein DNA DNA_with_flanks
Genetic context
GyrA context.png
This image was kindly provided by SubtiList
Expression at a glance   PubMed
GyrA expression.png















Categories containing this gene/protein

DNA condensation/ segregation, essential genes

This gene is a member of the following regulons

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:

Database entries

  • Structure:
    • 4DDQ (DNA gyrase A-subunit lacking the C-terminal DNA-wrapping domains) PubMed
  • 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

Markus G Rudolph, Dagmar Klostermeier
Mapping the spectrum of conformational states of the DNA- and C-gates in Bacillus subtilis gyrase.
J Mol Biol: 2013, 425(15);2632-40
[PubMed:23602808] [WorldCat.org] [DOI] (I p)

Luise A K Kleine Borgmann, Hanna Hummel, Maximilian H Ulbrich, Peter L Graumann
SMC condensation centers in Bacillus subtilis are dynamic structures.
J Bacteriol: 2013, 195(10);2136-45
[PubMed:23475963] [WorldCat.org] [DOI] (I p)

Nicole M Baker, Steven Weigand, Sarah Maar-Mathias, Alfonso Mondragón
Solution structures of DNA-bound gyrase.
Nucleic Acids Res: 2011, 39(2);755-66
[PubMed:20870749] [WorldCat.org] [DOI] (I p)

Airat Gubaev, Manuel Hilbert, Dagmar Klostermeier
The DNA-gate of Bacillus subtilis gyrase is predominantly in the closed conformation during the DNA supercoiling reaction.
Proc Natl Acad Sci U S A: 2009, 106(32);13278-83
[PubMed:19666507] [WorldCat.org] [DOI] (I p)

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)

Thomas Göttler, Dagmar Klostermeier
Dissection of the nucleotide cycle of B. subtilis DNA gyrase and its modulation by DNA.
J Mol Biol: 2007, 367(5);1392-404
[PubMed:17320901] [WorldCat.org] [DOI] (P p)

Jean-Christophe Meile, Ling Juan Wu, S Dusko Ehrlich, Jeff Errington, Philippe Noirot
Systematic localisation of proteins fused to the green fluorescent protein in Bacillus subtilis: identification of new proteins at the DNA replication factory.
Proteomics: 2006, 6(7);2135-46
[PubMed:16479537] [WorldCat.org] [DOI] (P 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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