Difference between revisions of "Sandbox"

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−
* '''Description:''' DEAD-box RNA helicase<br/><br/>
+
* '''Description:''' isochorismate synthase <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'''
−
|''deaD''
+
|''dhbC''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yxiN ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || ATP-dependent RNA helicase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || isochorismate synthase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA helicase
+
|style="background:#ABCDEF;" align="center"|'''Function''' || siderophore biosynthesis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 53 kDa, 7.706  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 43 kDa, 5.168  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1437 bp, 479 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1194 bp, 398 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yxiO]]'', ''[[yxiM]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dhbE]]'', ''[[dhbA]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15947&#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:CAB15189&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
 
|-
 
|-
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:deaD_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:dhbC_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 31: Line 31:
 
__TOC__
 
__TOC__
  
−
<br/><br/>
+
<br/><br/><br/><br/>
  
 
=The gene=
 
=The gene=
Line 37: Line 37:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU39110
+
* '''Locus tag:''' BSU31990
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 43: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yxiM-deaD.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dhbACEBF.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11143]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11242]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' RNA helicase
+
* '''Catalyzed reaction/ biological activity:''' Chorismate = isochorismate (according to Swiss-Prot)
  
−
* '''Protein family:''' DEAD-box RNA helicase
+
* '''Protein family:''' isochorismate synthase family (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):''' [[CshA]], [[CshB]], [[YfmL]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Domains:'''  
 
* '''Domains:'''  
−
**Helicase domain 1: AS 1-203
 
−
**Linker region: AS 204-212
 
−
**Helicase domain 2: AS 207-368
 
−
**RNA-binding domain: AS 404-479
 
  
−
* '''Modification:'''
+
* '''Modification:''' phosphorylation on Ser-271 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
Line 82: Line 78:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2G0C 2G0C] (RNA-binding domain, AA 404-479),  [http://www.rcsb.org/pdb/explore.do?structureId=2HJV 2HJV] (second domain, AA 207-368)
+
* '''Structure:'''
  
−
* '''Swiss prot entry:'''
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P45744 P45744]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU39110]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU31990]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/5.4.4.2 5.4.4.2]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[yxiM]]-[[deaD]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/10746760 PubMed]
+
* '''Operon:'''  
  
 
* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
Line 102: Line 98:
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP1121 (tet), available in the [[Stülke]] lab
+
* '''Mutant:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
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* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
+
* '''two-hybrid system:'''  
  
 
* '''Antibody:'''
 
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Dagmar Klostermeier]], Biozentrum Basel, Switzerland [http://www.biozentrum.unibas.ch/klostermeier/index.html homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
<pubmed>17142894 16118224 17229151, </pubmed>
+
<pubmed>17218307, </pubmed>
−
# Caruthers, J. M., Hu, Y. & McKay, D. B. (2006). Structure of the second domain of the ''Bacillus subtilis'' DEAD-box RNA helicase YxiN. Acta Crystallogr Sect F Struct Biol Cryst Commun 62, 1191-1195.[http://www.ncbi.nlm.nih.gov/pubmed/17142894 PubMed]
+
# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model  bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707  [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
−
# Karginov, F. V., Caruthers, J. M., Hu, Y., McKay, D. B. & Uhlenbeck, O. C. (2005). YxiN is a modular protein combining a DEx(D/H) core and a specific RNA-binding domain. J Biol Chem 280, 35499-35505.[http://www.ncbi.nlm.nih.gov/pubmed/16118224 PubMed]
 
−
# Karow, A. R., Theissen, B. & Klostermeier, D. (2007). Authentic interdomain communication in an RNA helicase reconstituted by expressed protein ligation of two helicase domains. FEBS J 274, 463-473.[http://www.ncbi.nlm.nih.gov/pubmed/17229151 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 13:15, 8 June 2009

  • Description: isochorismate synthase

Gene name dhbC
Synonyms
Essential no
Product isochorismate synthase
Function siderophore biosynthesis
MW, pI 43 kDa, 5.168
Gene length, protein length 1194 bp, 398 aa
Immediate neighbours dhbE, dhbA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
DhbC context.gif
This image was kindly provided by SubtiList





The gene

Basic information

  • Locus tag: BSU31990

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: Chorismate = isochorismate (according to Swiss-Prot)
  • Protein family: isochorismate synthase family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification: phosphorylation on Ser-271 PubMed
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • Structure:
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Operon:
  • 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

Boris Macek, Ivan Mijakovic, Jesper V Olsen, Florian Gnad, Chanchal Kumar, Peter R Jensen, Matthias Mann
The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis.
Mol Cell Proteomics: 2007, 6(4);697-707
[PubMed:17218307] [WorldCat.org] [DOI] (P p)

  1. Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 6: 697-707 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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