Dynamics on multiple timescales in the RNA-directed RNA polymerase from the cystovirus phi6

Nucleic Acids Res. 2010 Aug;38(15):5105-18. doi: 10.1093/nar/gkq210. Epub 2010 Apr 12.

Abstract

The de novo initiating RNA-directed RNA polymerase (RdRP), P2, forms the central machinery in the infection cycle of the bacteriophage phi6 by performing the dual tasks of replication and transcription of the double-stranded RNA genome in the host cell. By measurement and quantitative analysis of multiple-quantum spin-relaxation data for the delta1 positions of Ile residues that are distributed over the 3D-fold of P2, we find that the enzyme is dynamic both on the fast (ps-ns) and slow (micros-ms) timescales. The characteristics of several motional modes including those that coincide with the catalytic timescale (500-800/s) are altered in the presence of substrate analogs and single-stranded RNA templates. These studies reveal the plasticity of this finely tuned molecular machine and represent a first step towards linking structural information available from a host of crystal structures to catalytic mechanisms and timescales obtained from the measurements of kinetics for homologous systems in solution.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bacteriophage phi 6 / enzymology*
  • Guanosine Triphosphate / analogs & derivatives
  • Guanosine Triphosphate / metabolism
  • Isoleucine / chemistry
  • Molecular Dynamics Simulation
  • Nuclear Magnetic Resonance, Biomolecular
  • RNA / metabolism
  • RNA Replicase / chemistry*
  • RNA Replicase / metabolism

Substances

  • Isoleucine
  • 5'-guanylylmethylenebisphosphonate
  • RNA
  • Guanosine Triphosphate
  • RNA Replicase