Difference between revisions of "Sandbox"

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−
* '''Description:''' alkaline phosphatase A <br/><br/>
+
* '''Description:''' two-component response regulator, regulation of phosphate metabolism <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'''
−
|''phoB''
+
|''phoP''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''phoAIII ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || alkaline phosphatase A
+
|style="background:#ABCDEF;" align="center"| '''Product''' || two-component response regulator
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || aquisition of phosphate upon phosphoate starvation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of phosphate metabolism <br/>(phoA, phoB, phoD, resABCDE, tagAB, tagDEF, tuaA-H)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 5.895  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 27 kDa, 5.068  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1386 bp, 462 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 720 bp, 240 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ydhF]]'', ''[[ydhG]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[phoR]]'', ''[[mdh]]''
 
|-
 
|-
−
|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" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14871&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
 
|-
 
|-
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:phoB_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:phoP_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>
 
|-
 
|-
Line 31: Line 31:
 
__TOC__
 
__TOC__
  
−
<br/><br/>
+
<br/><br/><br/><br/>
  
 
=The gene=
 
=The gene=
Line 37: Line 37:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU05740
+
* '''Locus tag:''' BSU29110
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 43: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/phoB-ydhF.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/phoPR.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10697]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10363]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' A phosphate monoester + H<sub>2</sub>O = an alcohol + phosphate (according to Swiss-Prot)
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' alkaline phosphatase family (according to Swiss-Prot)
+
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[PhoA]]
+
* '''Paralogous protein(s):'''
 +
 
 +
=== Genes controlled by PhoP ===
 +
 
 +
* '''Activation by PhoP:''' ''[[phoP]]-[[phoR]]''
 +
 
 +
* '''Repression by PhoP:'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylated on ser/ thr/ tyr [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]  
+
* '''Modification:''' phosphorylation by [[PhoR]] under conditions of phosphate limitation (stimulates DNA-binding activity)
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[PhoP]]-[[PhoP]],  [[PhoP]]-[[PhoR]]
  
−
* '''Localization:''' extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
+
* '''Localization:''' cell membrane (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1MVO 1MVO] (receiver domain)
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P19405 P19405]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P13792 P13792]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU05740]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29110]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.3.1 3.1.3.1]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[phoB]]-[[ydhF]]''
+
* '''Operon:''' ''[[phoP]]-[[phoR]]''
  
−
* '''[[Sigma factor]]:''' [[SigA]], [[SigE]]
+
* '''[[Sigma factor]]:''' [[SigA]]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' repressed by glucose (4.3-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  induced by phosphate limitation ([[PhoP]]), carbon catabolite repression ([[CcpA]])
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression,  [[PhoP]]: transcription activation, [[CcpA]]: transcription repression
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 121: Line 127:
 
=References=
 
=References=
  
−
<pubmed>18957862 16493705, </pubmed>
+
<pubmed>12850135, </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]
+
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 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]
 
# 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: two-component response regulator, regulation of phosphate metabolism

Gene name phoP
Synonyms
Essential no
Product two-component response regulator
Function regulation of phosphate metabolism
(phoA, phoB, phoD, resABCDE, tagAB, tagDEF, tuaA-H)
MW, pI 27 kDa, 5.068
Gene length, protein length 720 bp, 240 aa
Immediate neighbours phoR, mdh
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
PhoP context.gif
This image was kindly provided by SubtiList





The gene

Basic information

  • Locus tag: BSU29110

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:
  • Paralogous protein(s):

Genes controlled by PhoP

  • Repression by PhoP:

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification: phosphorylation by PhoR under conditions of phosphate limitation (stimulates DNA-binding activity)
  • Cofactor(s):
  • Effectors of protein activity:
  • Localization: cell membrane (according to Swiss-Prot)

Database entries

  • Structure: 1MVO (receiver domain)
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation: repressed by glucose (4.3-fold) (CcpA) PubMed, induced by phosphate limitation (PhoP), carbon catabolite repression (CcpA)
  • Regulatory mechanism: CcpA: transcription repression, PhoP: transcription activation, CcpA: transcription repression
  • 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

Hans-Matti Blencke, Georg Homuth, Holger Ludwig, Ulrike Mäder, Michael Hecker, Jörg Stülke
Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways.
Metab Eng: 2003, 5(2);133-49
[PubMed:12850135] [WorldCat.org] [DOI] (P p)

  1. Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab Eng. 5: 133-149 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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