Difference between revisions of "Sandbox"

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#REDIRECT [[FadA]]
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* '''Description:''' ATP-dependent Clp protease, ATPase subunit <br/><br/>
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{| align="right" border="1" cellpadding="2"
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|-
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|style="background:#ABCDEF;" align="center"|'''Gene name'''
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|''clpC''
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|-
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''mecB ''
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|-
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no
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|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || ATP-dependent Clp protease, ATPase subunit
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|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || protein degradation
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positive regulator of autolysin ([[LytC]] and [[LytD]]) synthesis
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|-
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 89 kDa, 5.746 
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|-
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2430 bp, 810 aa
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|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mcsB]]'', ''[[radA]]''
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|-
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|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14213&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
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|-
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|colspan="2" | '''Genetic context''' <br/> [[Image:clpC_context.gif]]
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<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
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|-
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|}
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__TOC__
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<br/><br/><br/><br/>
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=The gene=
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 +
=== Basic information ===
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 +
* '''Coordinates:'''
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===Phenotypes of a mutant ===
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 +
=== Database entries ===
 +
 
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* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ctsR-mcsAB-clpC-radA-yacK.html]
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* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10148]
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 +
=== Additional information===
 +
 
 +
 
 +
=The protein=
 +
 
 +
=== Basic information/ Evolution ===
 +
 
 +
* '''Catalyzed reaction/ biological activity:''' ATPase/chaperone
 +
 
 +
* '''Protein family:''' mecA family (according to Swiss-Prot) clpA/clpB family. ClpC subfamily (according to Swiss-Prot), AAA+ -type ATPase (IPR013093) [http://www.ebi.ac.uk/interpro/IEntry?ac=IPR013093 InterPro] (PF07724) [http://pfam.sanger.ac.uk/family?acc=PF07724 PFAM]
 +
 
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* '''Paralogous protein(s):''' [[ClpE]], [[ClpX]]
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=== Extended information on the protein ===
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* '''Kinetic information:'''
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* '''Domains:''' AAA-ATPase [http://pfam.sanger.ac.uk/family?acc=PF07724 PFAM]
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* '''Modification:'''
 +
 
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* '''Cofactor(s):'''
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* '''Effectors of protein activity:'''
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 +
* '''Interactions:''' [[YpbH]]-[[ClpC]],  [[McsB]]-[[ClpC]],  [[ClpC]]-[[MecA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/10447896 PubMed],  [[ClpC]]-[[ClpP]]
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 +
* '''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:ClpC.jpg‎ ]]
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=== Database entries ===
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 +
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2K77 2K77] (N-terminal domain)
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 +
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P37571 P37571]
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 +
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00860 BSU00860]
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* '''E.C. number:'''
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 +
=== Additional information===
 +
 
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:* subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
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=Expression and regulation=
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 +
* '''Operon:''' ''[[ctsR]]-[[mcsA]]-[[mcsB]]-[[clpC]]-[[radA]]-[[disA]]'' [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed]
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* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed], [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed1] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed2]
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* '''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]
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* '''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]
 +
 
 +
* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
 +
 
 +
=Biological materials =
 +
 
 +
* '''Mutant:''' ''clpC::tet'' available from the [http://subtiwiki.uni-goettingen.de/wiki/index.php/Leendert_Hamoen Hamoen]] Lab
 +
 
 +
* '''Expression vector:'''
 +
       
 +
* '''lacZ fusion:'''
 +
 
 +
* '''GFP fusion:''' C-terminal GFP fusions (single copy, also as CFP and YFP variants) available from the [http://subtiwiki.uni-goettingen.de/wiki/index.php/Leendert_Hamoen Hamoen]] Lab
 +
 
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* '''two-hybrid system:'''
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* '''Antibody:'''
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=Labs working on this gene/protein=
 +
[[Leendert Hamoen]], Newcastle University, UK [http://www.ncl.ac.uk/camb/staff/profile/l.hamoen homepage]
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 +
=Your additional remarks=
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=References=
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<pubmed> 11544224, 17981983, 14763982, 18786145, 19361434 </pubmed>
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# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 16:03, 25 May 2009

  • Description: ATP-dependent Clp protease, ATPase subunit

Gene name clpC
Synonyms mecB
Essential no
Product ATP-dependent Clp protease, ATPase subunit
Function protein degradation

positive regulator of autolysin (LytC and LytD) synthesis

MW, pI 89 kDa, 5.746
Gene length, protein length 2430 bp, 810 aa
Immediate neighbours mcsB, radA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
ClpC context.gif
This image was kindly provided by SubtiList





The gene

Basic information

  • Coordinates:

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: mecA family (according to Swiss-Prot) clpA/clpB family. ClpC subfamily (according to Swiss-Prot), AAA+ -type ATPase (IPR013093) InterPro (PF07724) PFAM

Extended information on the protein

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

ClpC.jpg

Database entries

  • Structure: 2K77 (N-terminal domain)
  • E.C. number:

Additional information

  • subject to Clp-dependent proteolysis upon glucose starvation PubMed

Expression and regulation

  • Additional information: subject to Clp-dependent proteolysis upon glucose starvation PubMed

Biological materials

  • Mutant: clpC::tet available from the Hamoen] Lab
  • Expression vector:
  • lacZ fusion:
  • GFP fusion: C-terminal GFP fusions (single copy, 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

Douglas J Kojetin, Patrick D McLaughlin, Richele J Thompson, David Dubnau, Peter Prepiak, Mark Rance, John Cavanagh
Structural and motional contributions of the Bacillus subtilis ClpC N-domain to adaptor protein interactions.
J Mol Biol: 2009, 387(3);639-52
[PubMed:19361434] [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)

Ulf Gerth, Holger Kock, Ilja Kusters, Stephan Michalik, Robert L Switzer, Michael Hecker
Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis.
J Bacteriol: 2008, 190(1);321-31
[PubMed:17981983] [WorldCat.org] [DOI] (I p)

Holger Kock, Ulf Gerth, Michael Hecker
MurAA, catalysing the first committed step in peptidoglycan biosynthesis, is a target of Clp-dependent proteolysis in Bacillus subtilis.
Mol Microbiol: 2004, 51(4);1087-102
[PubMed:14763982] [WorldCat.org] [DOI] (P p)

A Petersohn, M Brigulla, S Haas, J D Hoheisel, U Völker, M Hecker
Global analysis of the general stress response of Bacillus subtilis.
J Bacteriol: 2001, 183(19);5617-31
[PubMed:11544224] [WorldCat.org] [DOI] (P p)


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