2W35

Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.259 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of Endonuclease V with DNA Reveal Initiation of Deaminated Adenine Repair.

Dalhus, B.Arvai, A.S.Rosnes, I.Olsen, O.E.Backe, P.H.Alseth, I.Gao, H.Cao, W.Tainer, J.A.Bjoras, M.

(2009) Nat Struct Mol Biol 16: 138

  • DOI: 10.1038/nsmb.1538
  • Primary Citation of Related Structures:  
    2W36, 2W35

  • PubMed Abstract: 
  • Endonuclease V (EndoV) initiates a major base-repair pathway for nitrosative deamination resulting from endogenous processes and increased by oxidative stress from mitochondrial dysfunction or inflammatory responses. We solved the crystal structures ...

    Endonuclease V (EndoV) initiates a major base-repair pathway for nitrosative deamination resulting from endogenous processes and increased by oxidative stress from mitochondrial dysfunction or inflammatory responses. We solved the crystal structures of Thermotoga maritima EndoV in complex with a hypoxanthine lesion substrate and with product DNA. The PYIP wedge motif acts as a minor groove-damage sensor for helical distortions and base mismatches and separates DNA strands at the lesion. EndoV incises DNA with an unusual offset nick 1 nucleotide 3' of the lesion, as the deaminated adenine is rotated approximately 90 degrees into a recognition pocket approximately 8 A from the catalytic site. Tight binding by the lesion-recognition pocket in addition to Mg(2+) and hydrogen-bonding interactions to the DNA ends stabilize the product complex, suggesting an orderly recruitment of downstream proteins in this base-repair pathway.


    Organizational Affiliation

    Centre for Molecular Biology and Neuroscience, Rikshospitalet University Hospital, Sognsvannsveien 20, N-0027 Oslo, Norway.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ENDONUCLEASE VAB225Thermotoga maritimaMutation(s): 0 
EC: 3.1.21.7
Find proteins for Q9X2H9 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Explore Q9X2H9 
Go to UniProtKB:  Q9X2H9
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*AP*TP*GP*CP*GP*AP*CP*IP*GP)-3'C, F9N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*AP*GP*CP*CP*GP*TP)-3'D, G6N/A
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      MG
      Query on MG

      Download CCD File 
      A, B
      MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.15 Å
      • R-Value Free: 0.288 
      • R-Value Work: 0.259 
      • R-Value Observed: 0.259 
      • Space Group: I 2 2 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 55.064α = 90
      b = 134.292β = 90
      c = 194.45γ = 90
      Software Package:
      Software NamePurpose
      CNSrefinement
      MOSFLMdata reduction
      SCALAdata scaling
      CNSphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2009-01-20
        Type: Initial release
      • Version 1.1: 2011-05-08
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance