Difference between revisions of "Sandbox"

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−
* '''Description:''' regulation of degradative enzyme production <br/><br/>
+
* '''Description:''' two-component sensor kinase for exoenzyme and competence regulation <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'''
−
|''degR''
+
|''degS''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''prtR ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''sacU ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || positive effector of DegU-phosphate stability
+
|style="background:#ABCDEF;" align="center"| '''Product''' || two-component sensor kinase (NarL family)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || control of DegU activity
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of degradative enzyme and genetic competence
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 6 kDa, 5.158  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 44 kDa, 5.988  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 180 bp, 60 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1155 bp, 385 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cspD]]'', ''[[ypzA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[degU]]'', ''[[yvyE]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14112&#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:CAB15567&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:degR_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:degS_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:''' BSU21940
+
* '''Locus tag:''' BSU35500
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/degR.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/degSU.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10699]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10392]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' ATP + protein L-histidine = ADP + protein N-phospho-L-histidine (according to Swiss-Prot) autophosphorylation, autodephosphorylation, phosphorylation of [[DegU]] on Asp-56 [http://www.ncbi.nlm.nih.gov/sites/entrez/1901568 PubMed]
  
 
* '''Protein family:'''
 
* '''Protein family:'''
Line 64: Line 64:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:'''
+
** aa  12 ... 170: unknown DegS domain
 +
** aa 180 ... 248: HisKA_3 domain (autophosphorylation)
 +
** aa 289 ... 384: HATPase_c
 +
 
 +
* '''Modification:''' phosphorylation on Ser-76 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed], autophosphorylation on His-189
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:'''
+
* '''Effectors of protein activity:''' [[DegQ]]
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[DegS]]-[[DegU]], [[DegS]]-[[DegQ]]
  
−
* '''Localization:''' cytoplasm (according to Swiss-Prot)
+
* '''Localization:''' Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P68731 P68731]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P13799 P13799]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU21940]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU35500]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[degR]]''
+
* '''Operon:''''' [[degS]]-[[degU]]''
  
−
* '''[[Sigma factor]]:''' [[SigD]]
+
* '''[[Sigma factor]]:''' [[SigA]]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' induced in the presence of ammonium ([[TnrA]])
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[TnrA]]: repression, [[DegU]]: positive autoregulation
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 113: Line 117:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Tarek Msadek]], Institut Pasteur, Paris, France
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
<pubmed>9335269,1459944,9108277,3098734,8550420,, </pubmed>
+
<pubmed>17850253,12471443,14563871,1459944,1901568,10094672,,16479537, 17218307 </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 09:02, 13 June 2009

  • Description: two-component sensor kinase for exoenzyme and competence regulation

Gene name degS
Synonyms sacU
Essential no
Product two-component sensor kinase (NarL family)
Function regulation of degradative enzyme and genetic competence
MW, pI 44 kDa, 5.988
Gene length, protein length 1155 bp, 385 aa
Immediate neighbours degU, yvyE
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
DegS context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU35500

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: ATP + protein L-histidine = ADP + protein N-phospho-L-histidine (according to Swiss-Prot) autophosphorylation, autodephosphorylation, phosphorylation of DegU on Asp-56 PubMed
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
    • aa 12 ... 170: unknown DegS domain
    • aa 180 ... 248: HisKA_3 domain (autophosphorylation)
    • aa 289 ... 384: HATPase_c
  • Modification: phosphorylation on Ser-76 PubMed, autophosphorylation on His-189
  • Cofactor(s):
  • Effectors of protein activity: DegQ
  • Localization: Cytoplasm (Homogeneous) PubMed

Database entries

  • Structure:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation: induced in the presence of ammonium (TnrA)
  • Regulatory mechanism: TnrA: repression, DegU: positive autoregulation
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Tarek Msadek, Institut Pasteur, Paris, France

Your additional remarks

References


  1. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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