3G0H

Human dead-box RNA helicase DDX19, in complex with an ATP-analogue and RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The DEXD/H-box RNA Helicase DDX19 Is Regulated by an {alpha}-Helical Switch.

Collins, R.Karlberg, T.Lehtio, L.Schutz, P.van den Berg, S.Dahlgren, L.G.Hammarstrom, M.Weigelt, J.Schuler, H.

(2009) J Biol Chem 284: 10296-10300

  • DOI: 10.1074/jbc.C900018200
  • Primary Citation of Related Structures:  
    3EWS, 3G0H

  • PubMed Abstract: 
  • DEXD/H-box RNA helicases couple ATP hydrolysis to RNA remodeling by an unknown mechanism. We used x-ray crystallography and biochemical analysis of the human DEXD/H-box protein DDX19 to investigate its regulatory mechanism. The crystal structures of DDX19, in its RNA-bound prehydrolysis and free posthydrolysis state, reveal an alpha-helix that inserts between the conserved domains of the free protein to negatively regulate ATPase activity ...

    DEXD/H-box RNA helicases couple ATP hydrolysis to RNA remodeling by an unknown mechanism. We used x-ray crystallography and biochemical analysis of the human DEXD/H-box protein DDX19 to investigate its regulatory mechanism. The crystal structures of DDX19, in its RNA-bound prehydrolysis and free posthydrolysis state, reveal an alpha-helix that inserts between the conserved domains of the free protein to negatively regulate ATPase activity. This finding was corroborated by biochemical data that confirm an autoregulatory function of the N-terminal region of the protein. This is the first study describing crystal structures of a DEXD/H-box protein in its open and closed cleft conformations.


    Organizational Affiliation

    Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-17177 Stockholm, Sweden.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent RNA helicase DDX19BA424Homo sapiensMutation(s): 0 
Gene Names: DBP5DDX19DDX19BTDBP
EC: 3.6.1 (PDB Primary Data), 3.6.4.13 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UMR2 (Homo sapiens)
Explore Q9UMR2 
Go to UniProtKB:  Q9UMR2
PHAROS:  Q9UMR2
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-R(P*UP*UP*UP*UP*UP*UP*U)-3'B [auth E]7N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ANP
    Query on ANP

    Download Ideal Coordinates CCD File 
    C [auth A]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
    C10 H17 N6 O12 P3
    PVKSNHVPLWYQGJ-KQYNXXCUSA-N
     Ligand Interaction
    GOL
    Query on GOL

    Download Ideal Coordinates CCD File 
    E [auth A]GLYCEROL
    C3 H8 O3
    PEDCQBHIVMGVHV-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    D [auth A]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.70 Å
    • R-Value Free: 0.275 
    • R-Value Work: 0.217 
    • R-Value Observed: 0.220 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 41.57α = 90
    b = 81.08β = 90
    c = 124.74γ = 90
    Software Package:
    Software NamePurpose
    MxCuBEdata collection
    PHASERphasing
    REFMACrefinement
    XDSdata reduction
    XSCALEdata scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Revision History  (Full details and data files)

    • Version 1.0: 2009-02-17
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Advisory, Version format compliance