DeaD

From SubtiWiki
Revision as of 17:23, 6 December 2009 by Jstuelk (talk | contribs) (References)
Jump to: navigation, search
  • 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)
  • 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

Regula Aregger, Dagmar Klostermeier
The DEAD box helicase YxiN maintains a closed conformation during ATP hydrolysis.
Biochemistry: 2009, 48(45);10679-81
[PubMed:19839642] [WorldCat.org] [DOI] (I p)

Anne R Karow, Dagmar Klostermeier
A conformational change in the helicase core is necessary but not sufficient for RNA unwinding by the DEAD box helicase YxiN.
Nucleic Acids Res: 2009, 37(13);4464-71
[PubMed:19474341] [WorldCat.org] [DOI] (I p)

Bettina Theissen, Anne R Karow, Jürgen Köhler, Airat Gubaev, Dagmar Klostermeier
Cooperative binding of ATP and RNA induces a closed conformation in a DEAD box RNA helicase.
Proc Natl Acad Sci U S A: 2008, 105(2);548-53
[PubMed:18184816] [WorldCat.org] [DOI] (I p)

Shuying Wang, Michael T Overgaard, YaoXiong Hu, David B McKay
The Bacillus subtilis RNA helicase YxiN is distended in solution.
Biophys J: 2008, 94(1);L01-3
[PubMed:17951299] [WorldCat.org] [DOI] (I p)

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)

Shuying Wang, Yaoxiong Hu, Michael T Overgaard, Fedor V Karginov, Olke C Uhlenbeck, David B McKay
The domain of the Bacillus subtilis DEAD-box helicase YxiN that is responsible for specific binding of 23S rRNA has an RNA recognition motif fold.
RNA: 2006, 12(6);959-67
[PubMed:16611943] [WorldCat.org] [DOI] (P 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)

Karl Kossen, Fedor V Karginov, Olke C Uhlenbeck
The carboxy-terminal domain of the DExDH protein YxiN is sufficient to confer specificity for 23S rRNA.
J Mol Biol: 2002, 324(4);625-36
[PubMed:12460566] [WorldCat.org] [DOI] (P p)

K Kossen, O C Uhlenbeck
Cloning and biochemical characterization of Bacillus subtilis YxiN, a DEAD protein specifically activated by 23S rRNA: delineation of a novel sub-family of bacterial DEAD proteins.
Nucleic Acids Res: 1999, 27(19);3811-20
[PubMed:10481020] [WorldCat.org] [DOI] (I p)