1DUC

EIAV DUTPASE DUDP/STRONTIUM COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1006/jmbi.1998.2332
  • Primary Citation of Related Structures:  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 d ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
A
134Equine infectious anemia virusGene Names: pol
EC: 3.1.-.-, 2.7.7.49, 3.1.26.13, 2.7.7.-, 3.1.13.2, 3.4.23.-
Find proteins for P11204 (Equine infectious anemia virus)
Go to UniProtKB:  P11204
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DUD
Query on DUD

Download SDF File 
Download CCD File 
A
DEOXYURIDINE-5'-DIPHOSPHATE
C9 H14 N2 O11 P2
QHWZTVCCBMIIKE-SHYZEUOFSA-N
 Ligand Interaction
SR
Query on SR

Download SDF File 
Download CCD File 
A
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.167 
  • Space Group: P 41 3 2
Unit Cell:
Length (Å)Angle (°)
a = 106.700α = 90.00
b = 106.700β = 90.00
c = 106.700γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-06-03
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Advisory