Difference between revisions of "Sandbox"

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#REDIRECT [[RemB]]
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* '''Description:''' DNA gyrase (subunit B) <br/><br/>
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{| align="right" border="1" cellpadding="2"
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|-
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|style="background:#ABCDEF;" align="center"|'''Gene name'''
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|''gyrB''
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|-
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''novA ''
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|-
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|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
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|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || DNA gyrase (subunit B)
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|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || DNA supercoiling, <br/>initation of replication cycle and DNA elongation
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|-
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|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]
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|-
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|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]
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|-
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 71 kDa, 5.378 
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|-
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1914 bp, 638 aa
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|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaB]]'', ''[[gyrA]]''
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|-
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|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]
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|-
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|colspan="2" | '''Genetic context''' <br/> [[Image:DnaA_dnaN_yaaA_recF_yaaB_gyrB_context.png]]
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<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
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|-
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|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]]
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|-
 +
|}
 +
 
 +
__TOC__
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<br/><br/><br/><br/>
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<br/><br/><br/><br/>
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<br/><br/><br/><br/>
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<br/><br/>
 +
 
 +
= [[Categories]] containing this gene/protein =
 +
{{SubtiWiki category|[[DNA condensation/ segregation]]}},
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{{SubtiWiki category|[[essential genes]]}}
 +
 
 +
= This gene is a member of the following [[regulons]] =
 +
 
 +
 
 +
=The gene=
 +
 
 +
=== Basic information ===
 +
 
 +
* '''Locus tag:''' BSU00060
 +
 
 +
===Phenotypes of a mutant ===
 +
 
 +
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 +
 
 +
=== Database entries ===
 +
 
 +
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yaaA-recF-yaaB-gyrB.html]
 +
 
 +
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10070]
 +
 
 +
=== 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:''' phosphorylated on Ser-400 {{PubMed|20509597}}
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* '''Cofactor(s):'''
 +
 
 +
* '''Effectors of protein activity:'''
 +
 
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* '''[[SubtInteract|Interactions]]:'''
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** [[GyrA]]-[[GyrB]]
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* '''[[Localization]]:'''
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** nucleoid-associated in actively growing cells [http://www.ncbi.nlm.nih.gov/sites/entrez/9539793 PubMed]
 +
 
 +
=== Database entries ===
 +
 
 +
* '''Structure:'''
 +
 
 +
* '''UniProt:''' [http://www.uniprot.org/uniprot/P05652 P05652]
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* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00060]
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* '''E.C. number:'''
 +
 
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=== Additional information===
 +
 
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=Expression and regulation=
 +
 
 +
* '''Operon:''' ''[[yaaA]]-[[recF]]-[[yaaB]]-[[gyrB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
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* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=gyrB_4867_6783_1 gyrB] {{PubMed|22383849}}
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* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
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* '''Regulation:'''
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* '''Regulatory mechanism:'''
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* '''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]
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=Biological materials =
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* '''Mutant:'''
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* '''Expression vector:'''
 +
       
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* '''lacZ fusion:'''
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* '''GFP fusion:'''
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* '''two-hybrid system:'''
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* '''Antibody:'''
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=Labs working on this gene/protein=
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 +
[[Dagmar Klostermeier]], Biozentrum Basel, Switzerland [http://www.biozentrum.unibas.ch/klostermeier/index.html homepage]
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=Your additional remarks=
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=References=
 +
'''Additional references:''' {{PubMed|20870749}}
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<pubmed>17981983 ,9539793 , 2987848 19666507 17320901  20509597 23475963</pubmed>
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 +
[[Category:Protein-coding genes]]

Revision as of 14:40, 11 November 2013

  • 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
Gene expression levels in SubtiExpress: GyrB
Interactions involving this protein in SubtInteract: GyrB
MW, pI 71 kDa, 5.378
Gene length, protein length 1914 bp, 638 aa
Immediate neighbours yaaB, gyrA
Sequences Protein DNA DNA_with_flanks
Genetic context
DnaA dnaN yaaA recF yaaB gyrB context.png
This image was kindly provided by SubtiList
Expression at a glance   PubMed
GyrB 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: 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: phosphorylated on Ser-400 PubMed
  • Cofactor(s):
  • Effectors of protein activity:

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

Additional references: PubMed

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)

Boumediene Soufi, Chanchal Kumar, Florian Gnad, Matthias Mann, Ivan Mijakovic, Boris Macek
Stable isotope labeling by amino acids in cell culture (SILAC) applied to quantitative proteomics of Bacillus subtilis.
J Proteome Res: 2010, 9(7);3638-46
[PubMed:20509597] [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)

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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