1OGL | pdb_00001ogl

The crystal structure of native Trypanosoma cruzi dUTPase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.263 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 1OGL

This is version 1.3 of the entry. See complete history

Literature

The Crystal Structure of Trypanosoma Cruzi Dutpase Reveals a Novel Dutp/Dudp Binding Fold

Harkiolaki, M.Dodson, E.J.Bernier-Villamor, V.Turkenburg, J.P.Gonzalez-Pacanowska, D.Wilson, K.S.

(2004) Structure 12: 41

  • DOI: https://doi.org/10.1016/j.str.2003.11.016
  • Primary Citation Related Structures: 
    1OGK, 1OGL

  • PubMed Abstract: 

    dUTPase is an essential enzyme involved with nucleotide metabolism and replication. We report here the X-ray structure of Trypanosoma cruzi dUTPase in its native conformation and as a complex with dUDP. These reveal a novel protein fold that displays no structural similarities to previously described dUTPases. The molecular unit is a dimer with two active sites. Nucleotide binding promotes extensive structural rearrangements, secondary structure remodeling, and rigid body displacements of 20 A or more, which effectively bury the substrate within the enzyme core for the purpose of hydrolysis. The molecular complex is a trapped enzyme-substrate arrangement which clearly demonstrates structure-induced specificity and catalytic potential. This enzyme is a novel dUTPase and therefore a potential drug target in the treatment of Chagas' disease.


  • Organizational Affiliation
    • Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, UK.

Macromolecule Content 

  • Total Structure Weight: 32.1 kDa 
  • Atom Count: 2,037 
  • Modeled Residue Count: 246 
  • Deposited Residue Count: 283 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DEOXYURIDINE TRIPHOSPHATASE283Trypanosoma cruziMutation(s): 0 
EC: 3.6.1.23
UniProt
Find proteins for O15923 (Trypanosoma cruzi)
Explore O15923 
Go to UniProtKB:  O15923
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15923
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.263 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.434α = 90
b = 136.434β = 90
c = 68.705γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
MLPHAREphasing
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-01-22
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references, Other, Refinement description