2PUS image
Deposition Date 2007-05-09
Release Date 2007-11-27
Last Version Date 2024-02-21
Entry Detail
PDB ID:
2PUS
Keywords:
Title:
Unprecedented activation mechanism of a non-canonical RNA-dependent RNA polymerase
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.40 Å
R-Value Free:
0.26
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
P 61 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:IBDV VP1 RNA-dependant RNA polymerase
Gene (Uniprot):VP1
Chain IDs:A
Chain Length:852
Number of Molecules:1
Biological Source:Infectious bursal disease virus
Primary Citation
Activation mechanism of a noncanonical RNA-dependent RNA polymerase.
Proc.Natl.Acad.Sci.Usa 104 20540 20545 (2007)
PMID: 18077388 DOI: 10.1073/pnas.0704447104

Abstact

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.

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Primary Citation of related structures