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

Experimental Data Snapshot

  • Resolution: 1.25 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.149 

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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: https://doi.org/10.1093/emboj/21.4.789
  • Primary Citation of Related Structures:  
    1K3W, 1K3X

  • 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 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.


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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Endonuclease VIIIC [auth A]262Escherichia coliMutation(s): 0 
Gene Names: nei
EC: 3.2.2
Find proteins for P50465 (Escherichia coli (strain K12))
Explore P50465 
Go to UniProtKB:  P50465
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50465
Sequence Annotations
  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*GP*GP*CP*(BRU)P*(BRU)P*CP*AP*(BRU)P*CP*CP*(BRU)P*GP*G)-3'A [auth B]13N/A
Sequence Annotations
  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3'B [auth C]13N/A
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • 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

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description