Difference between revisions of "Sandbox"

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−
* '''Description:''' ATP-dependent Clp protease proteolytic subunit (class III heat-shock protein) <br/><br/>
+
* '''Description:''' hypothetical 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''
+
|''coaX''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvdN ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yacB ''
 
|-
 
|-
 
|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''' || pantothenate kinase (EC 2.7.1.33)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || protein degradation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || coenyzmeA synthesis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 21 kDa, 5.008  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26 kDa, 8.37  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 591 bp, 197 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 699 bp, 233 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[trnQ-Arg]]'', ''[[pgcM]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ftsH]]'', ''[[yacC]]''
 
|-
 
|-
−
|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:CAB11846&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:clpP_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yacB_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:''' BSU00700
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/clpP.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG19016]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10133]
  
 
=== Additional information===
 
=== Additional information===
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=== 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:''' ATP + (R)-pantothenate = ADP + (R)-4'-phosphopantothenate (according to Swiss-Prot)  
  
−
* '''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:''' type III pantothenate kinase family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[ClpE]]-[[ClpP]],  [[ClpC]]-[[ClpP]], [[ClpX]]-[[ClpP]]
+
* '''Interactions:'''
  
−
* '''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:''' cytoplasm (according to Swiss-Prot)
−
 
 
−
[[File:ClpP.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:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P80244 P80244]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P37564 P37564]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU34540]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00700]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.4.21.92 3.4.21.92]
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.1.33 2.7.1.33]
  
 
=== 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:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
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* '''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:'''
  
 
* '''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>11544224 14763982 9643546, </pubmed>
+
<pubmed>15795230, </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]
+
# Leisl A. Brand and Erick Strauss (2005) Characterization of a New Pantothenate Kinase Isoform from Helicobacter pylori ''J Biol Chem.'' '''May 27;280(21):''' 20185-8. [http://www.ncbi.nlm.nih.gov/sites/entrez/15795230 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 13:59, 8 June 2009

  • Description: hypothetical protein

Gene name coaX
Synonyms yacB
Essential no
Product pantothenate kinase (EC 2.7.1.33)
Function coenyzmeA synthesis
MW, pI 26 kDa, 8.37
Gene length, protein length 699 bp, 233 aa
Immediate neighbours ftsH, yacC
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YacB context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU00700

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: ATP + (R)-pantothenate = ADP + (R)-4'-phosphopantothenate (according to Swiss-Prot)
  • Protein family: type III pantothenate kinase family (according to Swiss-Prot)
  • 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: [2]

Additional information

Expression and regulation

  • Operon:
  • Sigma factor:
  • 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. Leisl A. Brand and Erick Strauss (2005) Characterization of a New Pantothenate Kinase Isoform from Helicobacter pylori J Biol Chem. May 27;280(21): 20185-8. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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