Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' transcriptional repressor of ''[[citZ]]'' and ''[[citB]]'' <br/><br/>
+
* '''Description:''' ATP-dependent Clp protease proteolytic 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'''
−
|''ccpC''
+
|''clpP''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykuM ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvdN ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional repressor
+
|style="background:#ABCDEF;" align="center"| '''Product''' || ATP-dependent Clp protease proteolytic subunit
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of tricarboxylic acid branch of the TCA cycle
+
|style="background:#ABCDEF;" align="center"|'''Function''' || protein degradation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 5.932  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 21 kDa, 5.008  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 879 bp, 293 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 591 bp, 197 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykuL]]'', ''[[ykuN]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[trnQ-Arg]]'', ''[[pgcM]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13287&#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:CAB15459&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ccpC_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:clpP_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>
 
|-
 
|-
Line 35: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU14140
+
* '''Locus tag:''' BSU34540
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ykuJK-ykzF-ykuL-ccpC.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/clpP.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13297]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG19016]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' Hydrolysis of proteins to small peptides in the presence of ATP and magnesium (according to Swiss-Prot)  endopeptidase/proteolysis
  
−
* '''Protein family:'''
+
* '''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]
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
−
 
−
=== Genes controlled by CcpC ===
 
−
 
−
''[[citB]]'', ''[[citZ]]-[[icd]]-[[mdh]]''
 
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 74: Line 70:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[ClpE]]-[[ClpP]],  [[ClpC]]-[[ClpP]], [[ClpX]]-[[ClpP]]
 +
 
 +
* '''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]
  
−
* '''Localization:'''
+
[[File:ClpP.jpg‎ ]]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''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]
  
−
* '''Swiss prot entry:'''
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P80244 P80244]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU14140]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU34540]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.4.21.92 3.4.21.92]
  
 
=== Additional information===
 
=== Additional information===
Line 94: Line 92:
 
* '''Operon:'''  
 
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]
  
−
* '''Regulation:'''  
+
* '''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]
  
−
* '''Regulatory mechanism:'''  
+
* '''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:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''
+
* '''Mutant:''' ''clpP::spec'' and ''clpP::cat'' available from the [http://subtiwiki.uni-goettingen.de/wiki/index.php/Leendert_Hamoen Hamoen]] Lab
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 110: Line 108:
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
−
* '''GFP 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
  
 
* '''two-hybrid system:'''  
 
* '''two-hybrid system:'''  
Line 117: Line 115:
  
 
=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]
−
[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 124: Line 121:
 
=References=
 
=References=
  
−
<pubmed>10656796 12591885 11985717 14636591, </pubmed>
+
<pubmed>11544224 14763982 9643546, </pubmed>
−
# Jourlin-Castelli C, Mani N, Nakano MM, Sonenshein AL (2000) CcpC, a novel regulator of the LysR family required for glucose repression of the ''citB'' gene in ''Bacillus subtilis''. J Mol Biol 295:865-878. [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 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]
−
# Kim, H. J., S. I. Kim, M. Ratnayake-Lecamwasam, K. Tachikawa, A. L. Sonenshein, and M. Strauch. (2003) Complex regulation of the ''Bacillus subtilis'' aconitase gene. J. Bacteriol. 185:1672-1680. [http://www.ncbi.nlm.nih.gov/sites/entrez/12591885 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]
−
# Kim HJ, Jourlin-Castelli C, Kim SI, Sonenshein AL (2002a) Regulation of the ''Bacillus subtilis ccpC'' gene by CcpA and CcpC. Mol Microbiol 43:399-410. [http://www.ncbi.nlm.nih.gov/sites/entrez/11985717 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]
−
# Kim SI, Jourlin-Castelli C, Wellington SR, Sonenshein AL (2003) Mechanism of repression by ''Bacillus subtilis'' CcpC, a LysR family regulator. J Mol Biol 334:609-624. [http://www.ncbi.nlm.nih.gov/sites/entrez/14636591 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 13:59, 8 June 2009

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

Gene name clpP
Synonyms yvdN
Essential no
Product ATP-dependent Clp protease proteolytic subunit
Function protein degradation
MW, pI 21 kDa, 5.008
Gene length, protein length 591 bp, 197 aa
Immediate neighbours trnQ-Arg, pgcM
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
ClpP context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU34540

Phenotypes of a mutant

Database entries

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

Additional information

The protein

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
  • Protein family: peptidase S14 family (according to Swiss-Prot) ClpP (IPR001907) InterPro, (PF00574) PFAM
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Localization: cytoplasm (according to Swiss-Prot), cytoplasmic polar clusters, excluded from the nucleoid, induced clustering upon heatshock, colocalization with ClpX, ClpC and ClpE Pubmed

ClpP.jpg

Database entries

  • Structure: Two homologue structures resolved 1TYF, 1Y7O, structural model of B. subtilis ClpP available from hstrahl
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Operon:
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Leendert Hamoen, Newcastle University, UK homepage

Your additional remarks

References

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)

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. Petersohn et al. (2001) Global Analysis of the General Stress Response of Bacillus subtilis. J Bacteriol. 183: 5617-5631 PubMed
  2. 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. PubMed
  3. 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. PubMed
  4. 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
  5. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
Retrieved from "http://subtiwiki-test.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=89085"