DeaD

• Description: DEAD-box RNA helicase
  
  

Gene name	deaD
Synonyms	yxiN
Essential	no
Product	DEAD-box RNA helicase
Function	RNA helicase
Gene expression levels in SubtiExpress: deaD
Interactions involving this protein in SubtInteract: DeaD
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 This image was kindly provided by SubtiList
Expression at a glance   PubMed

Categories containing this gene/protein

DEAD-box RNA helicases, translation

The gene

Basic information

• Locus tag: BSU39110

Database entries

• DBTBS entry: [1]

• SubtiList entry: [2]

The protein

Basic information/ Evolution

• Catalyzed reaction/ biological activity: RNA helicase

• Protein family: DEAD-box RNA helicase

• Paralogous protein(s): CshA, CshB, YfmL

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:
  • DeaD-CshA PubMed
  • DeaD-CshB PubMed
  • DeaD-23S rRNA PubMed

• Localization:

Database entries

• Structure: 2G0C (RNA-binding domain, AA 404-479), 2HJV (second domain, AA 207-368); 3MOJ (RNA binding domain complexed with a fragment of 23S ribosomal RNA) PubMed

• UniProt: P42305

• KEGG entry: [3]

• E.C. number:

Expression and regulation

• Operon: yxiM-deaD PubMed

• Expression browser: deaD PubMed

• Sigma factor:

• Regulation:

• Regulatory mechanism:

• Additional information:

Biological materials

• Mutant: GP1052 (tet), available in the Stülke lab

• Expression vector:
  • for expression/ purification from B. subtilis with C-terminal Strep-tag, for SPINE, expression from the native chromomsomal site: GP1065 (spc), available in Jörg Stülke's lab

• lacZ fusion:

• GFP fusion:

• two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Jörg Stülke's lab

• FLAG-tag construct:
  • GP1068 (spc, based on pGP1331), available in Jörg Stülke's lab

• Antibody:

Labs working on this gene/protein

Dagmar Klostermeier, Biozentrum Basel, Switzerland homepage

References

Martin Lehnik-Habrink, Leonie Rempeters, Ákos T Kovács, Christoph Wrede, Claudia Baierlein, Heike Krebber, Oscar P Kuipers, Jörg Stülke
DEAD-Box RNA helicases in Bacillus subtilis have multiple functions and act independently from each other.
J Bacteriol: 2013, 195(3);534-44
[PubMed:23175651] [WorldCat.org] [DOI] (I p)

Anne R Karow, Dagmar Klostermeier
A structural model for the DEAD box helicase YxiN in solution: localization of the RNA binding domain.
J Mol Biol: 2010, 402(4);629-37
[PubMed:20691700] [WorldCat.org] [DOI] (I p)

John W Hardin, Yao Xiong Hu, David B McKay
Structure of the RNA binding domain of a DEAD-box helicase bound to its ribosomal RNA target reveals a novel mode of recognition by an RNA recognition motif.
J Mol Biol: 2010, 402(2);412-27
[PubMed:20673833] [WorldCat.org] [DOI] (I p)

Martin Lehnik-Habrink, Henrike Pförtner, Leonie Rempeters, Nico Pietack, Christina Herzberg, Jörg Stülke
The RNA degradosome in Bacillus subtilis: identification of CshA as the major RNA helicase in the multiprotein complex.
Mol Microbiol: 2010, 77(4);958-71
[PubMed:20572937] [WorldCat.org] [DOI] (I p)

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)