2W45

Epstein-Barr virus alkaline nuclease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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

  • 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALKALINE EXONUCLEASEA, B470Human gammaherpesvirus 4Mutation(s): 0 
EC: 3.1.11 (PDB Primary Data), 3.1 (UniProt)
UniProt
Find proteins for P03217 (Epstein-Barr virus (strain B95-8))
Explore P03217 
Go to UniProtKB:  P03217
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing

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