DeaD

• Description: DEAD-box RNA helicase, important for adaptation to low temperatures
  
  

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
Sequences	Protein DNA DNA_with_flanks
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

• BsubCyc: BSU39110

• DBTBS entry: [1]

• SubtiList entry: [2]

The protein

Basic information/ Evolution

• Catalyzed reaction/ biological activity:
  • RNA helicase
  • required for ribosome assembly PubMed

• 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

• BsubCyc: BSU39110

• 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:
  • expression declines in the stationary phase PubMed

• Regulatory mechanism:

• Additional information:
  • number of protein molecules per cell (minimal medium with glucose and ammonium): 96 PubMed

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

Lenz Steimer, Jan Philip Wurm, Martin H Linden, Markus G Rudolph, Jens Wöhnert, Dagmar Klostermeier
Recognition of two distinct elements in the RNA substrate by the RNA-binding domain of the T. thermophilus DEAD box helicase Hera.
Nucleic Acids Res: 2013, 41(12);6259-72
[PubMed:23625962] [WorldCat.org] [DOI] (I p)

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)