Activation mechanism of a noncanonical RNA-dependent RNA polymerase

doi:10.1073/pnas.0704447104

Activation mechanism of a noncanonical RNA-dependent RNA polymerase

*Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Cientificas, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain; and
^†Department of Molecular and Cell Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Cientificas, Calle Darwin Number 3, 28049 Madrid, Spain

Edited by Charles M. Rice III, The Rockefeller University, New York, NY, and approved October 22, 2007 (received for review May 11, 2007)

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 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 Mg²⁺ 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.

Footnotes

^¶To whom correspondence should be addressed. E-mail: nvmcri{at}ibmb.csic.es
Author contributions: D.G. and A.N. contributed equally to this work; J.F.R. and N.V. designed research; D.G., A.N., and J.Q.-A. performed research; A.N. and F.A. contributed new reagents/analytic tools; D.G., J.Q.-A., J.F.R., and N.V. analyzed data; and J.F.R. and N.V. wrote the paper.
↵ ^‡Present address: Kapsid Link S.L., Alcalá 420, 28017 Madrid, Spain.
↵ ^§Present address: Marie Curie Research Institute, The Chart, Oxted, Surrey RH8 OTL, United Kingdom.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
Data deposition: The atomic coordinates have been deposited in the Protein Data Bank, www.pdb.org (PDB ID codes 2PUS, 2QJ1, 2R70, and 2R72).
This article contains supporting information online at www.pnas.org/cgi/content/full/0704447104/DC1.