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 

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This is version 1.4 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: https://doi.org/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 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 ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Deoxyuridine 5'-triphosphate nucleotidohydrolase
A, B, C
164Homo sapiensMutation(s): 0 
Gene Names: DUTN, DUT
EC: 3.6.1.23
UniProt & NIH Common Fund Data Resources
Find proteins for P33316 (Homo sapiens)
Explore P33316 
Go to UniProtKB:  P33316
PHAROS:  P33316
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33316
Protein Feature View
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
DUP Binding MOAD:  2HQU Kd: 7200 (nM) from 1 assay(s)
PDBBind:  2HQU Kd: 7200 (nM) from 1 assay(s)
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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description