Difference between revisions of "Sandbox"

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* '''Description:''' ATP-dependent Clp protease, ATPase subunit <br/><br/>
+
* '''Description:''' ATP-dependent Clp protease-like (class III stress gene) <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'''
−
|''clpC''
+
|''clpE''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''mecB ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykvH ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || ATP-dependent Clp protease, ATPase subunit
+
|style="background:#ABCDEF;" align="center"| '''Product''' || ATP-dependent Clp protease-like
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || protein degradation
 
|style="background:#ABCDEF;" align="center"|'''Function''' || protein degradation
−
positive regulator of autolysin ([[LytC]] and [[LytD]]) synthesis
 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 89 kDa, 5.746 
+
|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"| '''Gene length, protein length''' || 2430 bp, 810 aa
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 77 kDa, 5.135 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mcsB]]'', ''[[radA]]''
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2097 bp, 699 aa
 
|-
 
|-
−
|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)'''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[motA]]'', ''[[ykvI]]''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:clpC_context.gif]]
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13243&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:clpE_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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__TOC__
 
__TOC__
  
−
<br/><br/><br/><br/>
+
<br/><br/><br/>
  
 
=The gene=
 
=The gene=
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU00860
+
* '''Locus tag:''' BSU13700
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ctsR-mcsAB-clpC-radA-yacK.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/clpE.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10148]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12578]
  
 
=== Additional information===
 
=== Additional information===
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' ATPase/chaperone
+
* '''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]
+
* '''Protein family:''' 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):''' [[ClpE]], [[ClpX]]
+
* '''Paralogous protein(s):''' [[ClpC]], [[ClpX]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[YpbH]]-[[ClpC]],  [[McsB]]-[[ClpC]],  [[ClpC]]-[[MecA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/10447896 PubMed],  [[ClpC]]-[[ClpP]]
+
* '''Interactions:''' [[ClpE]]-[[ClpP]]
  
−
* '''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:''' expressed after heat shock, localization in cytoplasmic polar clusters, excluded from the nucleoid, colocalization with [[ClpP]] [http://www.ncbi.nlm.nih.gov/pubmed/18786145 Pubmed]
−
[[File:ClpC.jpg‎ ]]
+
[[File:ClpE.jpg‎ ]]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2K77 2K77] (N-terminal domain)
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P37571 P37571]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O31673 O31673]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00860]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU13700]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=== Additional information===
 
=== 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]
 
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[ctsR]]-[[mcsA]]-[[mcsB]]-[[clpC]]-[[radA]]-[[disA]]'' [http://www.ncbi.nlm.nih.gov/pubmed/8793870 PubMed]
+
* '''Operon:'''  
  
−
* '''[[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]
+
* '''[[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:''' induced by heat ([[CtsR]]) [http://www.ncbi.nlm.nih.gov/pubmed/9987115 PubMed]
  
 
* '''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:''' [[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]
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' ''clpC::tet'' available from the [http://subtiwiki.uni-goettingen.de/wiki/index.php/Leendert_Hamoen Hamoen]] Lab  
+
* '''Mutant:''' ''clpE::spec'' available from the [http://subtiwiki.uni-goettingen.de/wiki/index.php/Leendert_Hamoen Hamoen]] Lab  
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
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* '''lacZ fusion:'''
 
* '''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  
+
* '''GFP fusion:''' C-terminal YFP and CFP fusions (single copy) available from the [http://subtiwiki.uni-goettingen.de/wiki/index.php/Leendert_Hamoen Hamoen]] Lab  
  
 
* '''two-hybrid system:'''  
 
* '''two-hybrid system:'''  
Line 121: Line 121:
  
 
=References=
 
=References=
−
 
+
# 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]
−
<pubmed> 11544224, 17981983, 14763982, 18786145, 19361434 </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 10:41, 11 June 2009

  • Description: ATP-dependent Clp protease-like (class III stress gene)

Gene name clpE
Synonyms ykvH
Essential no
Product ATP-dependent Clp protease-like
Function protein degradation
Metabolic function and regulation of this protein in SubtiPathways:
Stress
MW, pI 77 kDa, 5.135
Gene length, protein length 2097 bp, 699 aa
Immediate neighbours motA, ykvI
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
ClpE context.gif
This image was kindly provided by SubtiList




The gene

Basic information

  • Locus tag: BSU13700

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: 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: expressed after heat shock, localization in cytoplasmic polar clusters, excluded from the nucleoid, colocalization with ClpP Pubmed

ClpE.jpg

Database entries

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

Additional information

Expression and regulation

  • Operon:
  • Additional information:

Biological materials

  • Mutant: clpE::spec available from the Hamoen] Lab
  • Expression vector:
  • lacZ fusion:
  • GFP fusion: C-terminal YFP and CFP fusions (single copy) 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

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