Difference between revisions of "Sandbox"

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−
* '''Description:''' penicillin-binding protein I, D-alanyl-D-alanine carboxypeptidase <br/><br/>
+
* '''Description:''' DEAD-box RNA helicase<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'''
−
|''dacF''
+
|''deaD''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yxiN ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || penicillin-binding protein I, <br/>D-alanyl-D-alanine carboxypeptidase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || ATP-dependent RNA helicase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || carboxypeptidase
+
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA helicase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 43 kDa, 9.912  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 53 kDa, 7.706  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1167 bp, 389 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1437 bp, 479 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[spoIIAA]]'', ''[[punA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yxiO]]'', ''[[yxiM]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14280&#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:CAB15947&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:dacF_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:deaD_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/>
  
 
=The gene=
 
=The gene=
Line 35: Line 37:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU23480
+
* '''Locus tag:''' BSU39110
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dacF-spoIIAAB-sigF.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yxiM-deaD.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10295]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11143]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala (according to Swiss-Prot)
+
* '''Catalyzed reaction/ biological activity:''' RNA helicase
  
−
* '''Protein family:''' peptidase S11 family (according to Swiss-Prot)
+
* '''Protein family:''' DEAD-box RNA helicase
  
−
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[CshA]], [[CshB]], [[YfmL]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 63: Line 65:
  
 
* '''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:'''
Line 76: Line 82:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''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)
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P38422 P38422]
+
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU23480]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU39110]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 88: Line 94:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[dacF]]-[[spoIIAA]]-[[spoIIAB]]-[[sigF]]''
+
* '''Operon:''' ''[[yxiM]]-[[deaD]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/10746760 PubMed]
  
−
* '''[[Sigma factor]]:''' [[SigF]], [[SigG]]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed] ,  expressed during sporulation in the prespore [http://www.ncbi.nlm.nih.gov/sites/entrez/15758244 Link to a summary]
+
* '''Regulation:'''  
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
Line 100: Line 106:
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''
+
* '''Mutant:''' GP1121 (tet), available in the [[Stülke]] lab
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 108: Line 114:
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''two-hybrid system:'''  
+
* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
  
 
* '''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=
Line 118: Line 126:
 
=References=
 
=References=
  
−
<pubmed>12107147, </pubmed>
+
<pubmed>17142894 16118224 17229151, </pubmed>
−
# M&#228;der et al. (2002) Transcriptome and Proteome Analysis of ''Bacillus subtilis'' Gene Expression Modulated by Amino Acid Availability. ''J. Bacteriol'' '''184:''' 1844288-4295 [http://www.ncbi.nlm.nih.gov/pubmed/12107147 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]
 +
# 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: DEAD-box RNA helicase

Gene name deaD
Synonyms yxiN
Essential no
Product ATP-dependent RNA helicase
Function RNA helicase
MW, pI 53 kDa, 7.706
Gene length, protein length 1437 bp, 479 aa
Immediate neighbours yxiO, yxiM
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
DeaD context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU39110

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: RNA helicase
  • Protein family: DEAD-box RNA helicase

Extended information on the protein

  • Kinetic information:
  • 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:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • Structure: 2G0C (RNA-binding domain, AA 404-479), 2HJV (second domain, AA 207-368)
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant: GP1121 (tet), available in the Stülke lab
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Stülke lab
  • Antibody:

Labs working on this gene/protein

Dagmar Klostermeier, Biozentrum Basel, Switzerland homepage

Your additional remarks

References

Anne R Karow, Bettina Theissen, Dagmar Klostermeier
Authentic interdomain communication in an RNA helicase reconstituted by expressed protein ligation of two helicase domains.
FEBS J: 2007, 274(2);463-73
[PubMed:17229151] [WorldCat.org] [DOI] (P p)

Jonathan M Caruthers, YaoXiong Hu, David B McKay
Structure of the second domain of the Bacillus subtilis DEAD-box RNA helicase YxiN.
Acta Crystallogr Sect F Struct Biol Cryst Commun: 2006, 62(Pt 12);1191-5
[PubMed:17142894] [WorldCat.org] [DOI] (I p)

Fedor V Karginov, Jonathan M Caruthers, YaoXiong Hu, David B McKay, Olke C Uhlenbeck
YxiN is a modular protein combining a DEx(D/H) core and a specific RNA-binding domain.
J Biol Chem: 2005, 280(42);35499-505
[PubMed:16118224] [WorldCat.org] [DOI] (P p)

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