2W36

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.217 

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:  

  • 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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENDONUCLEASE V
A, B
225Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Mutation(s): 1 
Gene Names: nfi
EC: 3.1.21.7
Find proteins for Q9X2H9 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q9X2H9
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*CP*BRUP*AP*CP*IP*GP*AP*BRUP*CP*GP)-3'C,E11N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*CP*GP*AP*TP*CP*TP*GP*TP*AP*GP*CP)-3'D,F11N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
BRU
Query on BRU
C, E
DNA LINKINGC9 H12 Br N2 O8 PDU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.217 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 51.979α = 90.00
b = 132.239β = 90.00
c = 191.616γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SOLVEphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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