1OGK

The crystal structure of Trypanosoma cruzi dUTPase in complex with dUDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 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

  • Primary Citation of Related Structures:  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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DEOXYURIDINE TRIPHOSPHATASE
A, B, D, E
283Trypanosoma cruziGene Names: Tcdut
Find proteins for O15923 (Trypanosoma cruzi)
Go to UniProtKB:  O15923
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DUD
Query on DUD

Download SDF File 
Download CCD File 
B, D, E
DEOXYURIDINE-5'-DIPHOSPHATE
C9 H14 N2 O11 P2
QHWZTVCCBMIIKE-SHYZEUOFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 106.386α = 90.00
b = 50.307β = 101.35
c = 111.387γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-01-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance