Difference between revisions of "Sandbox"

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* '''Description:''' ATP-dependent Clp protease proteolytic subunit (class III heat-shock protein) <br/><br/>
+
* '''Description:''' ATP-dependent Clp protease ATP-binding subunit (class III heat-shock protein) <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'''
−
|''clpP''
+
|''clpX''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvdN ''
+
|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''' || ATP-dependent Clp protease proteolytic subunit
+
|style="background:#ABCDEF;" align="center"| '''Product''' || ATP-dependent Clp protease ATP-binding subunit
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || protein degradation
 
|style="background:#ABCDEF;" align="center"|'''Function''' || protein degradation
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|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''' || 21 kDa, 5.008  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46 kDa, 4.645  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 591 bp, 197 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1260 bp, 420 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[trnQ-Arg]]'', ''[[pgcM]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[lonB]]'', ''[[tig]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15459&#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:CAB14782&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:clpP_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:''' BSU34540
+
* '''Locus tag:''' BSU28220
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 43: Line 45:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/clpP.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/clpX.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG19016]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11387]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 56:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' Hydrolysis of proteins to small peptides in the presence of ATP and magnesium (according to Swiss-Prot)  endopeptidase/proteolysis
+
* '''Catalyzed reaction/ biological activity:''' ATPase/chaperone
  
−
* '''Protein family:''' peptidase S14 family (according to Swiss-Prot) ClpP (IPR001907) [http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR001907 InterPro], (PF00574) [http://pfam.sanger.ac.uk/family?acc=PF00574 PFAM]
+
* '''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]
  
−
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[ClpC]], [[ClpE]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Kinetic information:'''
 
* '''Kinetic information:'''
  
−
* '''Domains:'''  
+
* '''Domains:''' AAA-ATPase [http://pfam.sanger.ac.uk/family?acc=PF07724 PFAM], Zinc finger [http://pfam.sanger.ac.uk/family?acc=PF06689 PFAM]
  
 
* '''Modification:'''
 
* '''Modification:'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[ClpE]]-[[ClpP]],  [[ClpC]]-[[ClpP]], [[ClpX]]-[[ClpP]]
+
* '''Interactions:''' [[ClpP]]-[[ClpX]]
−
 
 
−
* '''Localization:''' cytoplasm (according to Swiss-Prot),  cytoplasmic polar clusters, excluded from the nucleoid, induced clustering upon heatshock, colocalization with [[ClpX]], [[ClpC]] and [[ClpE]] [http://www.ncbi.nlm.nih.gov/pubmed/18786145 Pubmed]  
 
  
−
[[File:ClpP.jpg‎ ]]
+
* '''Localization:''' cytoplasmic polar clusters, excluded from the nucleoid, induced clustering upon heatshock, colocalization with [[ClpP]] [http://www.ncbi.nlm.nih.gov/pubmed/18786145 Pubmed]
 +
[[File:ClpX.jpg‎ ]]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' Two homologue structures resolved [http://www.rcsb.org/pdb/explore/explore.do?structureId=1TYF 1TYF], [http://www.rcsb.org/pdb/explore/explore.do?structureId=1Y7O 1Y7O], structural model of ''B. subtilis'' [[ClpP]] available from [http://subtiwiki.uni-goettingen.de/wiki/index.php/User:Hstrahl hstrahl]
+
* '''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]
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P80244 P80244]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P50866 P50866]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU34540]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28220]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.4.21.92 3.4.21.92]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed], induced by heat ([[CtsR]]) [http://www.ncbi.nlm.nih.gov/pubmed/9987115 PubMed]
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' [[CtsR]]: transcription repression [http://www.ncbi.nlm.nih.gov/pubmed/9987115 PubMed1], [http://www.ncbi.nlm.nih.gov/pubmed/11179229 PubMed2], [http://www.ncbi.nlm.nih.gov/pubmed/16163393 PubMed3], [http://www.ncbi.nlm.nih.gov/pubmed/17380125 PubMed4]
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' ''clpP::spec'' and ''clpP::cat'' available from the [http://subtiwiki.uni-goettingen.de/wiki/index.php/Leendert_Hamoen Hamoen]] Lab  
+
* '''Mutant:''' ''clpX::kan'', ''clpX::spec'' and ''clpX::cat'' available from the [http://subtiwiki.uni-goettingen.de/wiki/index.php/Leendert_Hamoen Hamoen]] Lab  
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 110: Line 111:
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
−
* '''GFP fusion:''' C-terminal GFP fusions (both single copy and as 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:''' 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  
  
 
* '''two-hybrid system:'''  
 
* '''two-hybrid system:'''  
Line 123: Line 124:
 
=References=
 
=References=
  
−
<pubmed>11544224 14763982 9643546, </pubmed>
+
<pubmed> 19136590 , 9643546, 18786145 </pubmed>
−
# Petersohn et al. (2001) Global Analysis of the General Stress Response of ''Bacillus subtilis''. ''J Bacteriol.'' '''183:''' 5617-5631 [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]
+
 
−
# Kock H, Gerth U, Hecker M. (2004) MurAA, catalysing the first committed step in peptidoglycan biosynthesis, is a target of Clp-dependent proteolysis in Bacillus subtilis. Mol Microbiol, 51:1087-1102.  [http://www.ncbi.nlm.nih.gov/sites/entrez/14763982 PubMed]
 
−
# Gerth, U., Krüger, E., Derré, I., Msadek, T. and Hecker, M. 1998. Stress induction of the [[Bacillus subtilis clpP]] gene encoding a homologue of the proteolytic component of the ClpP protease and the involvement of ClpP and ClpX in stress tolerance. Mol. Microbiol. 28: 787-802. [http://www.ncbi.nlm.nih.gov/sites/entrez/9643546 PubMed]
 
−
# Kirstein, J., Strahl, H., Molière, N., Hamoen, LW., Turgay K. (2008) Localization of general and regulatory proteolysis in Bacillus subtilis cells. Mol Microbiol. 70:682-94. [http://www.ncbi.nlm.nih.gov/pubmed/18786145 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 11:42, 11 June 2009

  • Description: ATP-dependent Clp protease ATP-binding subunit (class III heat-shock protein)

Gene name clpX
Synonyms
Essential no
Product ATP-dependent Clp protease ATP-binding subunit
Function protein degradation
Metabolic function and regulation of this protein in SubtiPathways:
Stress
MW, pI 46 kDa, 4.645
Gene length, protein length 1260 bp, 420 aa
Immediate neighbours lonB, tig
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
ClpX context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU28220

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: ATPase/chaperone
  • Protein family: clpX chaperone family (according to Swiss-Prot) ClpX (IP004487) InterPro, AAA+ -type ATPase (IPR013093) InterPro (PF07724) PFAM

Extended information on the protein

  • Kinetic information:
  • Domains: AAA-ATPase PFAM, Zinc finger PFAM
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Localization: cytoplasmic polar clusters, excluded from the nucleoid, induced clustering upon heatshock, colocalization with ClpP Pubmed

ClpX.jpg

Database entries

  • Structure: homologue structure resolved 1UM8, structural model of B. subtilis ClpX available from hstrahl
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

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

Biological materials

  • Mutant: clpX::kan, clpX::spec and clpX::cat available from the Hamoen] Lab
  • Expression vector:
  • 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 Hamoen] Lab
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Leendert Hamoen, Newcastle University, UK homepage

Your additional remarks

References

Daniel P Haeusser, Amy H Lee, Richard B Weart, Petra Anne Levin
ClpX inhibits FtsZ assembly in a manner that does not require its ATP hydrolysis-dependent chaperone activity.
J Bacteriol: 2009, 191(6);1986-91
[PubMed:19136590] [WorldCat.org] [DOI] (I p)

Janine Kirstein, Henrik Strahl, Noël Molière, Leendert W Hamoen, Kürşad Turgay
Localization of general and regulatory proteolysis in Bacillus subtilis cells.
Mol Microbiol: 2008, 70(3);682-94
[PubMed:18786145] [WorldCat.org] [DOI] (I p)

U Gerth, E Krüger, I Derré, T Msadek, M Hecker
Stress induction of the Bacillus subtilis clpP gene encoding a homologue of the proteolytic component of the Clp protease and the involvement of ClpP and ClpX in stress tolerance.
Mol Microbiol: 1998, 28(4);787-802
[PubMed:9643546] [WorldCat.org] [DOI] (P p)


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