Epstein-Barr virus alkaline nuclease

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.197 

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This is version 1.3 of the entry. See complete history


A Bridge Crosses the Active Site Canyon of the Epstein-Barr Virus Nuclease with DNase and Rnase Activity.

Buisson, M.Geoui, T.Flot, D.Tarbouriech, N.Ressing, M.E.Wiertz, E.J.Burmeister, W.P.

(2009) J Mol Biol 391: 717

  • DOI: https://doi.org/10.1016/j.jmb.2009.06.034
  • Primary Citation of Related Structures:  
    2W45, 2W4B

  • PubMed Abstract: 

    Epstein-Barr virus, a double-stranded DNA (dsDNA) virus, is a major human pathogen from the herpesvirus family. The nuclease is one of the lytic cycle proteins required for successful viral replication. In addition to the previously described endonuclease and exonuclease activities on single-stranded DNA and dsDNA substrates, we observed an RNase activity for Epstein-Barr virus nuclease in the presence of Mn(2+), giving a possible explanation for its role in host mRNA degradation. Its crystal structure shows a catalytic core of the D-(D/E)XK nuclease superfamily closely related to the exonuclease from bacteriophage lambda with a bridge across the active-site canyon. This bridge may reduce endonuclease activity, ensure processivity or play a role in strand separation of dsDNA substrates. As the DNA strand that is subject to cleavage is likely to make a sharp turn in front of the bridge, endonuclease activity on single-stranded DNA stretches appears to be possible, explaining the cleavage of circular substrates.

  • Organizational Affiliation

    UMI UJF-EMBL-CNRS, Grenoble, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
470human gammaherpesvirus 4Mutation(s): 0 
EC: 3.1.11
Find proteins for P03217 (Epstein-Barr virus (strain B95-8))
Explore P03217 
Go to UniProtKB:  P03217
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03217
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.51α = 90
b = 63.787β = 93.59
c = 114.131γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-30
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-04-03
    Changes: Data collection, Other, Source and taxonomy