2PGG

Crystal Structure of a Birnavirus (IBDV) RNA-dependent RNA Polymerase VP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of a birnavirus polymerase reveals a distinct active site topology.

Pan, J.Vakharia, V.N.Tao, Y.J.

(2007) Proc.Natl.Acad.Sci.Usa 104: 7385-7390

  • DOI: 10.1073/pnas.0611599104

  • PubMed Abstract: 
  • Single-subunit polymerases are universally encoded in both cellular organisms and viruses. Their three-dimensional structures have the shape of a right-hand with the active site located in the palm region, which has a topology similar to that of the ...

    Single-subunit polymerases are universally encoded in both cellular organisms and viruses. Their three-dimensional structures have the shape of a right-hand with the active site located in the palm region, which has a topology similar to that of the RNA recognition motif (RRM) found in many RNA-binding proteins. Considering that polymerases have well conserved structures, it was surprising that the RNA-dependent RNA polymerases from birnaviruses, a group of dsRNA viruses, have their catalytic motifs arranged in a permuted order in sequence. Here we report the 2.5 A structure of a birnavirus VP1 in which the polymerase palm subdomain adopts a new active site topology that has not been previously observed in other polymerases. In addition, the polymerase motif C of VP1 has the sequence of -ADN-, a highly unusual feature for RNA-dependent polymerases. Through site-directed mutagenesis, we have shown that changing the VP1 motif C from -ADN- to -GDD- results in a mutant with an increased RNA synthesis activity. Our results indicate that the active site topology of VP1 may represent a newly developed branch in polymerase evolution, and that birnaviruses may have acquired the -ADN- mutation to control their growth rate.


    Organizational Affiliation

    Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77005, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-directed RNA polymerase
A
774Avian 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: 2.5 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.216 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 122.103α = 90.00
b = 122.103β = 90.00
c = 359.017γ = 120.00
Software Package:
Software NamePurpose
SHARPphasing
SCALEPACKdata scaling
DENZOdata reduction
CrystalCleardata collection
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-05-22
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance