Difference between revisions of "Sandbox"

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−
* '''Description:''' ATP-dependent Clp protease ATP-binding subunit (class III heat-shock protein) <br/><br/>
+
* '''Description:''' two-component response regulator, control of cellular responses to protein secretion stress <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'''
−
|''clpX''
+
|''cssR''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvqA ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || ATP-dependent Clp protease ATP-binding subunit
+
|style="background:#ABCDEF;" align="center"| '''Product''' || two-component response regulator
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || protein degradation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || control of cellular responses to protein secretion stress
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress]'''
 
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress]'''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46 kDa, 4.645  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26 kDa, 5.071  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1260 bp, 420 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 675 bp, 225 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[lonB]]'', ''[[tig]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[htrB]]'', ''[[cssS]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14782&#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:CAB15291&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:cssR_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:clpX_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:''' BSU28220
+
* '''Locus tag:''' BSU33010
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 45: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/clpX.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cssRS.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11387]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14131]
  
 
=== Additional information===
 
=== Additional information===
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' ATPase/chaperone
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' clpX chaperone family (according to Swiss-Prot) ClpX (IP004487) [http://www.ebi.ac.uk/interpro/IEntry?ac=IPR004487 InterPro], AAA+ -type ATPase (IPR013093) [http://www.ebi.ac.uk/interpro/IEntry?ac=IPR013093 InterPro] (PF07724) [http://pfam.sanger.ac.uk/family?acc=PF07724 PFAM]
+
* '''Protein family:''' OmpR family of two-component response regulators
  
−
* '''Paralogous protein(s):''' [[ClpC]], [[ClpE]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Kinetic information:'''
 
* '''Kinetic information:'''
  
−
* '''Domains:''' AAA-ATPase [http://pfam.sanger.ac.uk/family?acc=PF07724 PFAM], Zinc finger [http://pfam.sanger.ac.uk/family?acc=PF06689 PFAM]
+
* '''Domains:'''  
  
 
* '''Modification:'''
 
* '''Modification:'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[ClpP]]-[[ClpX]]
+
* '''Interactions:'''
  
−
* '''Localization:''' cytoplasmic polar clusters, excluded from the nucleoid, induced clustering upon heatshock, colocalization with [[ClpP]] [http://www.ncbi.nlm.nih.gov/pubmed/18786145 Pubmed]
+
* '''Localization:''' cytoplasm (according to Swiss-Prot)
−
[[File:ClpX.jpg‎ ]]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' homologue structure resolved [http://www.rcsb.org/pdb/explore/explore.do?structureId=1UM8 1UM8], structural model of ''B. subtilis'' ClpX available from [http://subtiwiki.uni-goettingen.de/wiki/index.php/User:Hstrahl hstrahl]
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P50866 P50866]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O32192 O32192]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28220]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33010]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' ''clpX::kan'', ''clpX::spec'' and ''clpX::cat'' available from the [http://subtiwiki.uni-goettingen.de/wiki/index.php/Leendert_Hamoen Hamoen]] Lab
+
* '''Mutant:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
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* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
−
* '''GFP fusion:''' C-terminal GFP fusions (both single copy and 2th copy in ''amyE'' locus, also as CFP and YFP variants) available from the [http://subtiwiki.uni-goettingen.de/wiki/index.php/Leendert_Hamoen Hamoen]] Lab
+
* '''GFP fusion:'''
  
 
* '''two-hybrid system:'''  
 
* '''two-hybrid system:'''  
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=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
[[Leendert Hamoen]], Newcastle University, UK [http://www.ncl.ac.uk/camb/staff/profile/l.hamoen homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
<pubmed> 19136590 , 9643546, 18786145 </pubmed>
+
<pubmed>12270824 11555295, </pubmed>
−
 
+
# Darmon E, Noone D, Masson A, Bron S, Kuipers OP, Devine KM, van Dijl JM. (2002) A novel class of heat and secretion stress-responsive genes is controlled by the autoregulated CssRS two-component system of Bacillus subtilis. ''J Bacteriol. '' '''184(20):''' 5661-71. [http://www.ncbi.nlm.nih.gov/sites/entrez/12270824 PubMed]
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
# Hyyryläinen HL, Bolhuis A, Darmon E, Muukkonen L, Koski P, Vitikainen M, Sarvas M, Prágai Z, Bron S, van Dijl JM, Kontinen VP. (2001) A novel two-component regulatory system in Bacillus subtilis for the survival of severe secretion stress. ''Mol Microbiol. '' '''41(5):''' 1159-72. [http://www.ncbi.nlm.nih.gov/sites/entrez/11555295 PubMed]

Revision as of 10:42, 11 June 2009

  • Description: two-component response regulator, control of cellular responses to protein secretion stress

Gene name cssR
Synonyms yvqA
Essential no
Product two-component response regulator
Function control of cellular responses to protein secretion stress
Metabolic function and regulation of this protein in SubtiPathways:
Stress
MW, pI 26 kDa, 5.071
Gene length, protein length 675 bp, 225 aa
Immediate neighbours htrB, cssS
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
CssR context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU33010

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: OmpR family of two-component response regulators
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

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

Additional information

Expression and regulation

  • Operon:
  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Your additional remarks

References

  1. Darmon E, Noone D, Masson A, Bron S, Kuipers OP, Devine KM, van Dijl JM. (2002) A novel class of heat and secretion stress-responsive genes is controlled by the autoregulated CssRS two-component system of Bacillus subtilis. J Bacteriol. 184(20): 5661-71. PubMed
  2. Hyyryläinen HL, Bolhuis A, Darmon E, Muukkonen L, Koski P, Vitikainen M, Sarvas M, Prágai Z, Bron S, van Dijl JM, Kontinen VP. (2001) A novel two-component regulatory system in Bacillus subtilis for the survival of severe secretion stress. Mol Microbiol. 41(5): 1159-72. PubMed
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