1K3X

Crystal structure of a trapped reaction intermediate of the DNA repair enzyme Endonuclease VIII with Brominated-DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.149 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural analysis of an Escherichia coli endonuclease VIII covalent reaction intermediate.

Zharkov, D.O.Golan, G.Gilboa, R.Fernandes, A.S.Gerchman, S.E.Kycia, J.H.Rieger, R.A.Grollman, A.P.Shoham, G.

(2002) EMBO J 21: 789-800

  • DOI: 10.1093/emboj/21.4.789
  • Primary Citation of Related Structures:  
    1K3X, 1K3W

  • PubMed Abstract: 
  • Endonuclease VIII (Nei) of Escherichia coli is a DNA repair enzyme that excises oxidized pyrimidines from DNA. Nei shares with formamidopyrimidine-DNA glycosylase (Fpg) sequence homology and a similar mechanism of action: the latter involves removal ...

    Endonuclease VIII (Nei) of Escherichia coli is a DNA repair enzyme that excises oxidized pyrimidines from DNA. Nei shares with formamidopyrimidine-DNA glycosylase (Fpg) sequence homology and a similar mechanism of action: the latter involves removal of the damaged base followed by two sequential beta-elimination steps. However, Nei differs significantly from Fpg in substrate specificity. We determined the structure of Nei covalently crosslinked to a 13mer oligodeoxynucleotide duplex at 1.25 A resolution. The crosslink is derived from a Schiff base intermediate that precedes beta-elimination and is stabilized by reduction with NaBH(4). Nei consists of two domains connected by a hinge region, creating a DNA binding cleft between domains. DNA in the complex is sharply kinked, the deoxyribitol moiety is bound covalently to Pro1 and everted from the duplex into the active site. Amino acids involved in substrate binding and catalysis are identified. Molecular modeling and analysis of amino acid conservation suggest a site for recognition of the damaged base. Based on structural features of the complex and site-directed mutagenesis studies, we propose a catalytic mechanism for Nei.


    Organizational Affiliation

    Novosibirsk Institute of Bioorganic Chemistry, Siberian Division of Russian Academy of Sciences, Novosibirsk 630090, Russia.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Endonuclease VIIIA262Escherichia coliMutation(s): 0 
Gene Names: nei
EC: 3.2.2 (PDB Primary Data), 4.2.99.18 (UniProt)
Find proteins for P50465 (Escherichia coli (strain K12))
Explore P50465 
Go to UniProtKB:  P50465
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*GP*CP*(BRU)P*(BRU)P*CP*AP*(BRU)P*CP*CP*(BRU)P*GP*G)-3'B13N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3'C13N/A
      Small Molecules
      Ligands 3 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      SO4
      Query on SO4

      Download CCD File 
      A
      SULFATE ION
      O4 S
      QAOWNCQODCNURD-UHFFFAOYSA-L
       Ligand Interaction
      GOL
      Query on GOL

      Download CCD File 
      A
      GLYCEROL
      C3 H8 O3
      PEDCQBHIVMGVHV-UHFFFAOYSA-N
       Ligand Interaction
      ZN
      Query on ZN

      Download CCD File 
      A
      ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.25 Å
      • R-Value Free: 0.181 
      • R-Value Work: 0.149 
      • Space Group: P 43 2 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 76.495α = 90
      b = 76.495β = 90
      c = 164.31γ = 90
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      SHELXmodel building
      SHELXL-97refinement
      SHELXphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2002-10-04
        Type: Initial release
      • Version 1.1: 2008-04-27
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Non-polymer description, Version format compliance