Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' putative immunity 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'''
−
|''ybgB''
+
|''clpX''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
Line 10: Line 10:
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Product''' || ATP-dependent Clp protease ATP-binding subunit
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+
|style="background:#ABCDEF;" align="center"|'''Function''' || protein degradation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 10 kDa, 8.47 
+
|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''' || 273 bp, 91 aa
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46 kDa, 4.645 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybgA]]'', ''[[ybgE]]''
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1260 bp, 420 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:CAB12032&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[lonB]]'', ''[[tig]]''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:ybgB_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:CAB14782&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 +
|-
 +
|-
 +
|-
 +
|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>
 
|-
 
|-
Line 35: Line 39:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU02380
+
* '''Locus tag:''' BSU28220
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 45:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ybgB.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/clpX.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12748]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11387]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 56:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' ATPase/chaperone
  
−
* '''Protein family:'''
+
* '''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 ===
Line 62: Line 66:
 
* '''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:'''
Line 70: Line 74:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:'''
+
* '''Interactions:''' [[ClpP]]-[[ClpX]]
  
−
* '''Localization:''' cell membrane (according to Swiss-Prot)
+
* '''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:'''
+
* '''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/O31460 O31460]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P50866 P50866]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU02380]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU28220]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 100: Line 105:
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''
+
* '''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 106: Line 111:
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
−
* '''GFP 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 [http://subtiwiki.uni-goettingen.de/wiki/index.php/Leendert_Hamoen Hamoen]] Lab
  
 
* '''two-hybrid system:'''  
 
* '''two-hybrid system:'''  
Line 113: Line 118:
  
 
=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=
  
 
=References=
 
=References=
 +
 +
<pubmed> 19136590 , 9643546, 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 20:49, 12 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


  1. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
Retrieved from "http://subtiwiki-test.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=92554"