Residues Arg283, Arg285, and Ile287 in the nucleotide binding pocket of bovine viral diarrhea virus NS5B RNA polymerase affect catalysis and fidelity

J Virol. 2013 Jan;87(1):199-207. doi: 10.1128/JVI.06968-11. Epub 2012 Oct 17.

Abstract

Residues Arg283, Arg285, and Ile287 are highly conserved amino acids in bovine viral diarrhea virus RNA polymerase (BVDV RdRp) and RdRps from related positive-strand RNA viruses. This motif is an important part of the binding pocket for the nascent RNA base pair during initiation and elongation. We found that replacement of the arginines with alanines or more conserved lysines or replacement of isoleucine with alanine or valine alters the ability of the mutant RdRps to incorporate ribonucleotides efficiently. The reduced RdRp activity stems from both decreased ribonucleotide binding and decreased catalytic efficiency in both primer-dependent and de novo initiation, as shown by kinetic studies. In line with other studies on flaviviral RdRps, our data suggest that Arg283 and Ile287 may be implicated in ribonucleotide binding and positioning of the template base in the active site. Arg285 appears to be involved directly in the selection of cognate nucleotide. The findings for Arg285 and Ile287 mutants also agree with similar data from picornavirus RdRps.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs*
  • Amino Acid Substitution
  • Amino Acids / genetics*
  • Animals
  • Binding Sites
  • Cattle
  • DNA-Directed RNA Polymerases / genetics
  • DNA-Directed RNA Polymerases / metabolism*
  • Diarrhea Viruses, Bovine Viral / enzymology*
  • Diarrhea Viruses, Bovine Viral / genetics
  • Kinetics
  • Mutagenesis, Site-Directed
  • Protein Binding
  • Ribonucleotides / metabolism

Substances

  • Amino Acids
  • Ribonucleotides
  • DNA-Directed RNA Polymerases