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 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.7554/eLife.09832
  • Primary Citation of Related Structures:  
    5EAN, 5EAW, 5EAX, 5EAY

  • 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 2.3 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

    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication ATP-dependent helicase/nuclease DNA21,059Mus musculusMutation(s): 0 
Gene Names: Dna2Dna2lKiaa0083
EC: 3.1 (PDB Primary Data), 3.6.4.12 (PDB Primary Data)
UniProt
Find proteins for Q6ZQJ5 (Mus musculus)
Explore Q6ZQJ5 
Go to UniProtKB:  Q6ZQJ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6ZQJ5
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*CP*TP*CP*TP*GP*CP*CP*AP*AP*GP*AP*GP*GP*A)-3')15Mus musculus
Sequence Annotations
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  • Reference Sequence
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

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Ligand Structure Quality Assessment 


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
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description