Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.159 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Crystal structure of dUTPase from equine infectious anaemia virus; active site metal binding in a substrate analogue complex.

Dauter, Z.Persson, R.Rosengren, A.M.Nyman, P.O.Wilson, K.S.Cedergren-Zeppezauer, E.S.

(1999) J Mol Biol 285: 655-673

  • DOI: https://doi.org/10.1006/jmbi.1998.2332
  • Primary Citation of Related Structures:  
    1DUC, 1DUN

  • PubMed Abstract: 

    The X-ray structures of dUTPase from equine infectious anaemia virus (EIAV) in unliganded and complexed forms have been determined to 1.9 and 2.0 A resolution, respectively. The structures were solved by molecular replacement using Escherichia coli dUTPase as search model. The exploitation of a relatively novel refinement approach for the initial model, combining maximum likelihood refinement with stereochemically unrestrained updating of the model, proved to be of crucial importance and should be of general relevance.EIAV dUTPase is a homotrimer where each subunit folds into a twisted antiparallel beta-barrel with the N and C-terminal portions interacting with adjacent subunits. The C-terminal 14 and 17 amino acid residues are disordered in the crystal structure of the unliganded and complexed enzyme, respectively. Interactions along the 3-fold axis include a water-containing volume (size 207 A3) which has no contact with bulk solvent. It has earlier been shown that a divalent metal ion is essential for catalysis. For the first time, a putative binding site for such a metal ion, in this case Sr2+, is established. The positions of the inhibitor (the non-hydrolysable substrate analogue dUDP) and the metal ion in the complex are consistent with the location of the active centre established for trimeric dUTPase structures, in which subunit interfaces form three surface clefts lined with evolutionary conserved residues. However, a detailed comparison of the active sites of the EIAV and E. coli enzymes reveals some structural differences. The viral enzyme undergoes a small conformational change in the uracil-binding beta-hairpin structure upon dUDP binding not observed in the other known dUTPase structures.

  • Organizational Affiliation

    Department of Chemistry, University of York, Heslington, YO1 5DD, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE134Equine infectious anemia virusMutation(s): 0 
EC: (PDB Primary Data), 3.4.23 (UniProt), (UniProt), (UniProt), (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P11204 (Equine infectious anemia virus (isolate 1369))
Explore P11204 
Go to UniProtKB:  P11204
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11204
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.159 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.27α = 90
b = 86.27β = 90
c = 95.24γ = 120
Software Package:
Software NamePurpose

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-05-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Advisory, Derived calculations, Other