4DK2

Crystal Structure of Open Trypanosoma brucei dUTPase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

On the catalytic mechanism of dimeric dUTPases.

Hemsworth, G.R.Gonzalez-Pacanowska, D.Wilson, K.S.

(2013) Biochem.J. 456: 81-88

  • DOI: 10.1042/BJ20130796
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Tritryps Trypanosoma brucei, Trypanosoma cruzi and Leishmania donovani are responsible for great morbidity and mortality in developing countries. Their dimeric dUTPases are members of the all-α NTP pyrophosphohydrolase family and represent promis ...

    The Tritryps Trypanosoma brucei, Trypanosoma cruzi and Leishmania donovani are responsible for great morbidity and mortality in developing countries. Their dimeric dUTPases are members of the all-α NTP pyrophosphohydrolase family and represent promising drug targets due to their essential nature and markedly different structural and biochemical properties compared with the trimeric human enzyme. In the present paper we describe the structure of the T. brucei enzyme in open and closed conformations. Furthermore, we probe the reaction mechanism through the binding of transition state mimics both in solution and in the crystal. 31P-NMR and tryptophan fluorescence quenching in the presence of AlF3 and MgF3- identified which phosphate is subject to nucleophilic attack by a water molecule. The structures in complex with two transition state analogues confirm that the nucleophilic attack occurs on the β-phosphate in contrast with the α-phosphate in the trimeric enzymes. These results establish the structural basis of catalysis of these important housekeeping enzymes and has ramifications for the wider all-α NTP pyrophosphohydrolase family.


    Organizational Affiliation

    *Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Deoxyuridine triphosphatase
A
297Trypanosoma brucei brucei (strain 927/4 GUTat10.1)Mutation(s): 0 
EC: 3.6.1.23
Find proteins for Q57ZH3 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Go to UniProtKB:  Q57ZH3
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.178 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 94.010α = 90.00
b = 47.020β = 89.38
c = 63.460γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-07
    Type: Initial release
  • Version 1.1: 2013-09-18
    Type: Database references
  • Version 1.2: 2013-11-06
    Type: Database references