2R70

Crystal structure of infectious bursal disease virus VP1 polymerase, cocrystallized with an oligopeptide mimicking the VP3 C-terminus.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Activation mechanism of a noncanonical RNA-dependent RNA polymerase.

Garriga, D.Navarro, A.Querol-Audi, J.Abaitua, F.Rodriguez, J.F.Verdaguer, N.

(2007) Proc.Natl.Acad.Sci.Usa 104: 20540-20545

  • DOI: 10.1073/pnas.0704447104
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Two lineages of viral RNA-dependent RNA polymerases (RDRPs) differing in the organization (canonical vs. noncanonical) of the palm subdomain have been identified. Phylogenetic analyses indicate that both lineages diverged at a very early stage of the ...

    Two lineages of viral RNA-dependent RNA polymerases (RDRPs) differing in the organization (canonical vs. noncanonical) of the palm subdomain have been identified. Phylogenetic analyses indicate that both lineages diverged at a very early stage of the evolution of the enzyme [Gorbalenya AE, Pringle FM, Zeddam JL, Luke BT, Cameron CE, Kalmakoff J, Hanzlik TN, Gordon KH, Ward VK (2002) J Mol Biol 324:47-62]. Here, we report the x-ray structure of a noncanonical birnaviral RDRP, named VP1, in its free form, bound to Mg(2+) ions, and bound to a peptide representing the polymerase-binding motif of the regulatory viral protein VP3. The structure of VP1 reveals that the noncanonical connectivity of the palm subdomain maintains the geometry of the catalytic residues found in canonical polymerases but results in a partial blocking of the active site cavity. The VP1-VP3 peptide complex shows a mode of polymerase activation in which VP3 binding promotes a conformational change that removes the steric blockade of the VP1 active site, facilitating the accommodation of the template and incoming nucleotides for catalysis. The striking structural similarities between birnavirus (dsRNA) and the positive-stranded RNA picornavirus and calicivirus RDRPs provide evidence supporting the existence of functional and evolutionary relationships between these two virus groups.


    Organizational Affiliation

    Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Cientificas, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
INFECTIOUS BURSAL VIRUS VP1 POLYMERASE
A
852Avian infectious bursal disease virusMutation(s): 0 
Gene Names: VP1
EC: 2.7.7.48
Find proteins for Q9Q6Q5 (Avian infectious bursal disease virus)
Go to UniProtKB:  Q9Q6Q5
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.221 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 123.801α = 90.00
b = 123.801β = 90.00
c = 361.843γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALAdata scaling
REFMACphasing
REFMACrefinement
MOSFLMdata reduction
DNAdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-11-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance