2WE1

EBV dUTPase mutant Asp131Asn with bound dUMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The Flexible Motif V of Epstein-Barr Virus Deoxyuridine 5'-Triphosphate Pyrophosphatase is Essential for Catalysis.

Freeman, L.Buisson, M.Tarbouriech, N.Van Der Heyden, A.Labbe, P.Burmeister, W.P.

(2009) J Biol Chem 284: 25280

  • DOI: 10.1074/jbc.M109.019315
  • Primary Citation of Related Structures:  
    2WE0, 2WE1, 2WE2, 2WE3

  • PubMed Abstract: 
  • Deoxyuridine 5'-triphosphate pyrophosphatases (dUTPases) are ubiquitous enzymes essential for hydrolysis of dUTP, thus preventing its incorporation into DNA. Although Epstein-Barr virus (EBV) dUTPase is monomeric, it has a high degree of similarity with the more frequent trimeric form of the enzyme ...

    Deoxyuridine 5'-triphosphate pyrophosphatases (dUTPases) are ubiquitous enzymes essential for hydrolysis of dUTP, thus preventing its incorporation into DNA. Although Epstein-Barr virus (EBV) dUTPase is monomeric, it has a high degree of similarity with the more frequent trimeric form of the enzyme. In both cases, the active site is composed of five conserved sequence motifs. Structural and functional studies of mutants based on the structure of EBV dUTPase gave new insight into the mechanism of the enzyme. A first mutant allowed us to exclude a role in enzymatic activity for the disulfide bridge involving the beginning of the disordered C terminus. Sequence alignments revealed two groups of dUTPases, based on the position in sequence of a conserved aspartic acid residue close to the active site. Single mutants of this residue in EBV dUTPase showed a highly impaired catalytic activity, which could be partially restored by a second mutation, making EBV dUTPase more similar to the second group of enzymes. Deletion of the flexible C-terminal tail carrying motif V resulted in a protein completely devoid of enzymatic activity, crystallizing with unhydrolyzed Mg(2+)-dUTP complex in the active site. Point mutations inside motif V highlighted the essential role of lid residue Phe(273). Magnesium appears to play a role mainly in substrate binding, since in absence of Mg(2+), the K(m) of the enzyme is reduced, whereas the k(cat) is less affected.


    Related Citations: 
    • The Monomeric Dutpase from Epstein-Barr Virus Mimics Trimeric Dutpases.
      Tarbouriech, N., Buisson, M., Seigneurin, J.M., Cusack, S., Burmeister, W.P.
      (2005) Structure 13: 1299

    Organizational Affiliation

    Unit of Virus Host Cell Interactions UMI3265 UJF-EMBL-CNRS, University of Grenoble, F-38042 Grenoble Cedex 9, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASEA286Human herpesvirus 4 strain B95-8Mutation(s): 1 
Gene Names: DUTBLLF3
EC: 3.6.1.23
UniProt
Find proteins for P03195 (Epstein-Barr virus (strain B95-8))
Explore P03195 
Go to UniProtKB:  P03195
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03195
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UMP
Query on UMP

Download Ideal Coordinates CCD File 
B [auth A]2'-DEOXYURIDINE 5'-MONOPHOSPHATE
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.624α = 90
b = 56.859β = 90
c = 81.073γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-07
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance