Difference between revisions of "Sandbox"

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−
* '''Description:''' beta-lactamase <br/><br/>
+
* '''Description:''' transcriptional repressor of the peroxide regulon <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'''
−
|''penP''
+
|''perR''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ygaG ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || beta-lactamase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional repressor
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || resistance to beta-lactam antibiotics
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of the response to peroxide
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 9.208  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 16 kDa, 5.888  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 918 bp, 306 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 435 bp, 145 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yoaZ]]'', ''[[yobA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ygaF]]'', ''[[ygzB]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13772&#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:CAB12701&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:penP_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:perR_context.gif]]
 
  <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:''' BSU18800
+
* '''Locus tag:''' BSU08730
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/perR.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11016]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12227]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' A beta-lactam + H<sub>2</sub>O = a substituted beta-amino acid (according to Swiss-Prot)
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:'''
+
* '''Protein family:''' Fur family (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[Zur]], [[Fur]]
 +
 
 +
=== Genes repressed by PerR ===
 +
 
 +
''[[ahpC]]-[[ahpF]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/11532148 PubMed], ''[[zosA]]''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
+
* '''Localization:''' cytoplasm (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2RGV 2RGV]
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39824 P39824]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P71086 P71086]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU18800]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU08730]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.5.2.6 3.5.2.6]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:'''  
+
* '''Regulation:''' negative autoregulation [http://www.ncbi.nlm.nih.gov/sites/entrez/12029044 PubMed]
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' repressed by '''PerR''' [http://www.ncbi.nlm.nih.gov/sites/entrez/12029044 PubMed]
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 113: Line 117:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
[[John Helmann]], Cornell University, USA [http://www.micro.cornell.edu/research/labs/helmann-lab/index.cfm Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 118: Line 123:
 
=References=
 
=References=
  
−
<pubmed>18957862, </pubmed>
+
<pubmed>11532148 12029044, </pubmed>
−
# Voigt et al. (2009) Cell physiology and protein secretion of ''Bacillus licheniformis'' compared to ''Bacillus subtilis''. ''J Mol Microbiol Biotechnol.'' '''16:''' 53-68 [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
+
# Herbig AF, Helmann JD. (2001) Roles of metal ions and hydrogen peroxide in modulating the interaction of the Bacillus subtilis PerR peroxide regulon repressor with operator DNA. ''Mol Microbiol.'' '''Aug;41(4):''' 849-59. [http://www.ncbi.nlm.nih.gov/sites/entrez/11532148 PubMed]
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
# Fuangthong M, Herbig AF, Bsat N, Helmann JD. (2002) Regulation of the Bacillus subtilis fur and perR genes by PerR: not all members of the PerR regulon are peroxide inducible. ''J Bacteriol.'' '''Jun;184(12):''' 3276-86.[http://www.ncbi.nlm.nih.gov/sites/entrez/12029044 PubMed]

Revision as of 13:28, 8 June 2009

  • Description: transcriptional repressor of the peroxide regulon

Gene name perR
Synonyms ygaG
Essential no
Product transcriptional repressor
Function regulation of the response to peroxide
MW, pI 16 kDa, 5.888
Gene length, protein length 435 bp, 145 aa
Immediate neighbours ygaF, ygzB
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
PerR context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU08730

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family: Fur family (according to Swiss-Prot)
  • Paralogous protein(s): Zur, Fur

Genes repressed by PerR

ahpC-ahpF PubMed, zosA

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: cytoplasm (according to Swiss-Prot)

Database entries

  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Regulation: negative autoregulation PubMed
  • Regulatory mechanism: repressed by PerR PubMed
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

John Helmann, Cornell University, USA Homepage

Your additional remarks

References

Mayuree Fuangthong, Andrew F Herbig, Nada Bsat, John D Helmann
Regulation of the Bacillus subtilis fur and perR genes by PerR: not all members of the PerR regulon are peroxide inducible.
J Bacteriol: 2002, 184(12);3276-86
[PubMed:12029044] [WorldCat.org] [DOI] (P p)

A F Herbig, J D Helmann
Roles of metal ions and hydrogen peroxide in modulating the interaction of the Bacillus subtilis PerR peroxide regulon repressor with operator DNA.
Mol Microbiol: 2001, 41(4);849-59
[PubMed:11532148] [WorldCat.org] [DOI] (P p)

  1. Herbig AF, Helmann JD. (2001) Roles of metal ions and hydrogen peroxide in modulating the interaction of the Bacillus subtilis PerR peroxide regulon repressor with operator DNA. Mol Microbiol. Aug;41(4): 849-59. PubMed
  2. Fuangthong M, Herbig AF, Bsat N, Helmann JD. (2002) Regulation of the Bacillus subtilis fur and perR genes by PerR: not all members of the PerR regulon are peroxide inducible. J Bacteriol. Jun;184(12): 3276-86.PubMed
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