6FWR

Structure of DinG in complex with ssDNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report



Literature

DNA translocation mechanism of an XPD family helicase.

Cheng, K.Wigley, D.B.

(2018) Elife 7

  • DOI: 10.7554/eLife.42400
  • Primary Citation of Related Structures:  
    6FWR, 6FWS

  • PubMed Abstract: 
  • The XPD family of helicases, that includes human disease-related FANCJ, DDX11 and RTEL1, are Superfamily two helicases that contain an iron-sulphur cluster domain, translocate on ssDNA in a 5'-3' direction and play important roles in genome stability ...

    The XPD family of helicases, that includes human disease-related FANCJ, DDX11 and RTEL1, are Superfamily two helicases that contain an iron-sulphur cluster domain, translocate on ssDNA in a 5'-3' direction and play important roles in genome stability. Consequently, mutations in several of these family members in eukaryotes cause human diseases. Family members in bacteria, such as the DinG helicase from Escherichia coli , are also involved in DNA repair. Here we present crystal structures of complexes of DinG bound to single-stranded DNA (ssDNA) in the presence and absence of an ATP analogue (ADP•BeF 3 ), that suggest a mechanism for 5'-3' translocation along the ssDNA substrate. This proposed mechanism has implications for how those enzymes of the XPD family that recognise bulky DNA lesions might stall at these as the first step in initiating DNA repair. Biochemical data reveal roles for conserved residues that are mutated in human diseases.


    Organizational Affiliation

    Section of Structural Biology, Department of Medicine, Imperial College London, London, United Kingdom.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent DNA helicase DinGA716Escherichia coliMutation(s): 0 
Gene Names: dinGCV83915_00780
EC: 3.6.4.12
Find proteins for P27296 (Escherichia coli (strain K12))
Explore P27296 
Go to UniProtKB:  P27296
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')B11synthetic construct
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    SF4
    Query on SF4

    Download CCD File 
    A
    IRON/SULFUR CLUSTER
    Fe4 S4
    LJBDFODJNLIPKO-VKOJMFJBAC
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.50 Å
    • R-Value Free: 0.246 
    • R-Value Work: 0.211 
    • R-Value Observed: 0.212 
    • Space Group: P 21 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 98.971α = 90
    b = 133.867β = 90
    c = 58.862γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    xia2data reduction
    xia2data scaling
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    Medical Research Council and Cancer Research UKUnited KingdomMR/N009258/1

    Revision History 

    • Version 1.0: 2018-12-19
      Type: Initial release