4A4D

Crystal structure of the N-terminal domain of the Human DEAD-BOX RNA helicase DDX5 (P68)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.262 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The Variable N-Terminal Region of Ddx5 Contains Structural Elements and Auto-Inhibits its Interaction with Ns5B of Hepatitis C Virus.

Dutta, S.Gupta, G.Choi, Y.W.Kotaka, M.Fielding, B.C.Song, J.Tan, Y.J.

(2012) Biochem.J. 446: 37

  • DOI: 10.1042/BJ20120001

  • PubMed Abstract: 
  • RNA helicases of the DEAD (Asp-Glu-Ala-Asp)-box family of proteins are involved in many aspects of RNA metabolism from transcription to RNA decay, but most of them have also been shown to be multifunctional. The DEAD-box helicase DDX5 of host cells h ...

    RNA helicases of the DEAD (Asp-Glu-Ala-Asp)-box family of proteins are involved in many aspects of RNA metabolism from transcription to RNA decay, but most of them have also been shown to be multifunctional. The DEAD-box helicase DDX5 of host cells has been shown to interact with the RNA-dependent RNA polymerase (NS5B) of HCV (hepatitis C virus). In the present study, we report the presence of two independent NS5B-binding sites in DDX5, one located at the N-terminus and another at the C-terminus. The N-terminal fragment of DDX5, which consists of the first 305 amino acids and shall be referred as DDX5-N, was expressed and crystallized. The crystal structure shows that domain 1 (residues 79-303) of DDX5 contains the typical features found in the structures of other DEAD-box helicases. DDX5-N also contains the highly variable NTR (N-terminal region) of unknown function and the crystal structure reveals structural elements in part of the NTR, namely residues 52-78. This region forms an extensive loop and an α-helix. From co-immunoprecipitation experiments, the NTR of DDX5-N was observed to auto-inhibit its interaction with NS5B. Interestingly, the α-helix in NTR is essential for this auto-inhibition and seems to mediate the interaction between the highly flexible 1-51 residues in NTR and the NS5B-binding site in DDX5-N. Furthermore, NMR investigations reveal that there is a direct interaction between DDX5 and NS5B in vitro.


    Organizational Affiliation

    Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore 138673.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROBABLE ATP-DEPENDENT RNA HELICASE DDX5
A
253Homo sapiensMutation(s): 0 
Gene Names: DDX5 (G17P1, HELR, HLR1)
EC: 3.6.4.13
Find proteins for P17844 (Homo sapiens)
Go to Gene View: DDX5
Go to UniProtKB:  P17844
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.262 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 66.180α = 90.00
b = 73.801β = 90.00
c = 104.000γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling
MrBUMPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-08
    Type: Initial release