5EAN

Crystal structure of Dna2 in complex with a 5' overhang DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Dna2 nuclease-helicase structure, mechanism and regulation by Rpa.

Zhou, C.Pourmal, S.Pavletich, N.P.

(2015) Elife 4

  • DOI: 10.7554/eLife.09832
  • Primary Citation of Related Structures:  
    5EAN, 5EAY, 5EAX, 5EAW

  • PubMed Abstract: 
  • The Dna2 nuclease-helicase maintains genomic integrity by processing DNA double-strand breaks, Okazaki fragments and stalled replication forks. Dna2 requires ssDNA ends, and is dependent on the ssDNA-binding protein Rpa, which controls cleavage polarity. Here we present the 2 ...

    The Dna2 nuclease-helicase maintains genomic integrity by processing DNA double-strand breaks, Okazaki fragments and stalled replication forks. Dna2 requires ssDNA ends, and is dependent on the ssDNA-binding protein Rpa, which controls cleavage polarity. Here we present the 2.3 Å structure of intact mouse Dna2 bound to a 15-nucleotide ssDNA. The nuclease active site is embedded in a long, narrow tunnel through which the DNA has to thread. The helicase domain is required for DNA binding but not threading. We also present the structure of a flexibly-tethered Dna2-Rpa interaction that recruits Dna2 to Rpa-coated DNA. We establish that a second Dna2-Rpa interaction is mutually exclusive with Rpa-DNA interactions and mediates the displacement of Rpa from ssDNA. This interaction occurs at the nuclease tunnel entrance and the 5' end of the Rpa-DNA complex. Hence, it only displaces Rpa from the 5' but not 3' end, explaining how Rpa regulates cleavage polarity.


    Organizational Affiliation

    Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, United States.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication ATP-dependent helicase/nuclease DNA2 A1059Mus musculusMutation(s): 0 
Gene Names: Dna2Dna2lKiaa0083
EC: 3.1 (PDB Primary Data), 3.6.4.12 (PDB Primary Data)
Find proteins for Q6ZQJ5 (Mus musculus)
Explore Q6ZQJ5 
Go to UniProtKB:  Q6ZQJ5
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*AP*CP*TP*CP*TP*GP*CP*CP*AP*AP*GP*AP*GP*GP*A)-3')B15Mus musculus
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ADP
    Query on ADP

    Download Ideal Coordinates CCD File 
    A
    ADENOSINE-5'-DIPHOSPHATE
    C10 H15 N5 O10 P2
    XTWYTFMLZFPYCI-KQYNXXCUSA-N
     Ligand Interaction
    SF4
    Query on SF4

    Download Ideal Coordinates CCD File 
    A
    IRON/SULFUR CLUSTER
    Fe4 S4
    LJBDFODJNLIPKO-VKOJMFJBAC
     Ligand Interaction
    CA
    Query on CA

    Download Ideal Coordinates CCD File 
    A, B
    CALCIUM ION
    Ca
    BHPQYMZQTOCNFJ-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.36 Å
    • R-Value Free: 0.246 
    • R-Value Work: 0.208 
    • R-Value Observed: 0.209 
    • Space Group: P 2 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 87.153α = 90
    b = 118.488β = 90
    c = 149.26γ = 90
    Software Package:
    Software NamePurpose
    HKL-2000data scaling
    REFMACrefinement
    PDB_EXTRACTdata extraction
    SCALEPACKdata scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2015-11-18
      Type: Initial release
    • Version 1.1: 2017-11-22
      Changes: Derived calculations, Refinement description