2HQU

Human dUTPase in complex with alpha,beta-iminodUTP and magnesium ion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Active site closure facilitates juxtaposition of reactant atoms for initiation of catalysis by human dUTPase.

Varga, B.Barabas, O.Kovari, J.Toth, J.Hunyadi-Gulyas, E.Klement, E.Medzihradszky, K.F.Tolgyesi, F.Fidy, J.Vertessy, B.G.

(2007) FEBS Lett 581: 4783-4788

  • DOI: 10.1016/j.febslet.2007.09.005
  • Primary Citation of Related Structures:  
    2HQU

  • PubMed Abstract: 
  • Human dUTPase, essential for DNA integrity, is an important survival factor for cancer cells. We determined the crystal structure of the enzyme:alpha,beta-imino-dUTP:Mg complex and performed equilibrium binding experiments in solution. Ordering of th ...

    Human dUTPase, essential for DNA integrity, is an important survival factor for cancer cells. We determined the crystal structure of the enzyme:alpha,beta-imino-dUTP:Mg complex and performed equilibrium binding experiments in solution. Ordering of the C-terminus upon the active site induces close juxtaposition of the incoming nucleophile attacker water oxygen and the alpha-phosphorus of the substrate, decreasing their distance below the van der Waals limit. Complex interactions of the C-terminus with both substrate and product were observed via a specifically designed tryptophan sensor, suitable for further detailed kinetic and ligand binding studies. Results explain the key functional role of the C-terminus.


    Related Citations: 
    • Human dUTP pyrophosphatase: uracil recognition by a beta hairpin and active sites formed by three separate subunits.
      Mol, C.D., Harris, J.M., McIntosh, E.M., Tainer, J.A.
      (1996) Structure 4: 1077

    Organizational Affiliation

    Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Deoxyuridine 5'-triphosphate nucleotidohydrolaseABC164Homo sapiensMutation(s): 0 
Gene Names: DUTNDUT
EC: 3.6.1.23
Find proteins for P33316 (Homo sapiens)
Explore P33316 
Go to UniProtKB:  P33316
NIH Common Fund Data Resources
PHAROS  P33316
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DUP
Query on DUP

Download CCD File 
A, B, C
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
C9 H16 N3 O13 P3
XZLLMTSKYYYJLH-SHYZEUOFSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DUPKd:  1600   nM  Binding MOAD
DUPKd :  7200   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.409α = 90
b = 71.773β = 90
c = 76.475γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-07-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.3: 2016-10-19
    Changes: Refinement description