Difference between revisions of "Sandbox"

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−
* '''Description:''' transcriptional repressor of the peroxide regulon <br/><br/>
+
* '''Description:''' alkaline phosphatase 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'''
−
|''perR''
+
|''phoB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ygaG ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''phoAIII ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional repressor
+
|style="background:#ABCDEF;" align="center"| '''Product''' || alkaline phosphatase A
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of the response to peroxide
+
|style="background:#ABCDEF;" align="center"|'''Function''' || aquisition of phosphate upon phosphoate starvation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 16 kDa, 5.888  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 5.895  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 435 bp, 145 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1386 bp, 462 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ygaF]]'', ''[[ygzB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ydhF]]'', ''[[ydhG]]''
 
|-
 
|-
−
|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" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12393&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:perR_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:phoB_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:''' BSU08730
+
* '''Locus tag:''' BSU05740
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/perR.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/phoB-ydhF.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12227]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10697]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' A phosphate monoester + H<sub>2</sub>O = an alcohol + phosphate (according to Swiss-Prot)  
−
 
 
−
* '''Protein family:''' Fur family (according to Swiss-Prot)
 
−
 
 
−
* '''Paralogous protein(s):''' [[Zur]], [[Fur]]
 
  
−
=== Genes repressed by PerR ===
+
* '''Protein family:''' alkaline phosphatase family (according to Swiss-Prot)
  
−
''[[ahpC]]-[[ahpF]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/11532148 PubMed], ''[[zosA]]''
+
* '''Paralogous protein(s):''' [[PhoA]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:'''
+
* '''Modification:''' phosphorylated on ser/ thr/ tyr [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' cytoplasm (according to Swiss-Prot)
+
* '''Localization:''' extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2RGV 2RGV]
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P71086 P71086]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P19405 P19405]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU08730]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU05740]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.3.1 3.1.3.1]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[phoB]]-[[ydhF]]''
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigA]], [[SigE]]
  
−
* '''Regulation:''' negative autoregulation [http://www.ncbi.nlm.nih.gov/sites/entrez/12029044 PubMed]
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' repressed by '''PerR''' [http://www.ncbi.nlm.nih.gov/sites/entrez/12029044 PubMed]
+
* '''Regulatory mechanism:'''  
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 117: Line 115:
  
 
=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]
+
[[Marion Hulett]], University of Illinois at Chicago, USA [http://www.uic.edu/depts/bios/faculty/hulett/hulettm.shtml Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
<pubmed>11532148 12029044, </pubmed>
+
<pubmed>18957862 16493705, </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]
+
# 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]
−
# 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]
+
# L&#233;vine et al. (2006) Analysis of the dynamic ''Bacillus subtilis'' Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. ''Proteomics'' '''6:''' 2157-2173 [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
 +
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 13:29, 8 June 2009

  • Description: alkaline phosphatase A

Gene name phoB
Synonyms phoAIII
Essential no
Product alkaline phosphatase A
Function aquisition of phosphate upon phosphoate starvation
MW, pI 50 kDa, 5.895
Gene length, protein length 1386 bp, 462 aa
Immediate neighbours ydhF, ydhG
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
PhoB context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU05740

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: A phosphate monoester + H2O = an alcohol + phosphate (according to Swiss-Prot)
  • Protein family: alkaline phosphatase family (according to Swiss-Prot)
  • Paralogous protein(s): PhoA

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification: phosphorylated on ser/ thr/ tyr PubMed
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: extracellular (signal peptide) PubMed

Database entries

  • Structure:
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Marion Hulett, University of Illinois at Chicago, USA Homepage

Your additional remarks

References

Birgit Voigt, Haike Antelmann, Dirk Albrecht, Armin Ehrenreich, Karl-Heinz Maurer, Stefan Evers, Gerhard Gottschalk, Jan Maarten van Dijl, Thomas Schweder, Michael Hecker
Cell physiology and protein secretion of Bacillus licheniformis compared to Bacillus subtilis.
J Mol Microbiol Biotechnol: 2009, 16(1-2);53-68
[PubMed:18957862] [WorldCat.org] [DOI] (I p)

Alain Lévine, Françoise Vannier, Cédric Absalon, Lauriane Kuhn, Peter Jackson, Elaine Scrivener, Valérie Labas, Joëlle Vinh, Patrick Courtney, Jérôme Garin, Simone J Séror
Analysis of the dynamic Bacillus subtilis Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes.
Proteomics: 2006, 6(7);2157-73
[PubMed:16493705] [WorldCat.org] [DOI] (P p)

  1. Voigt et al. (2009) Cell physiology and protein secretion of Bacillus licheniformis compared to Bacillus subtilis. J Mol Microbiol Biotechnol. 16: 53-68 PubMed
  2. Lévine et al. (2006) Analysis of the dynamic Bacillus subtilis Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. Proteomics 6: 2157-2173 PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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