Crystal structure of the RNA-dependent RNA polymerase from hepatitis C virus reveals a fully encircled active site

Nat Struct Biol. 1999 Oct;6(10):937-43. doi: 10.1038/13305.


Various classes of nucleotidyl polymerases with different transcriptional roles contain a conserved core structure. Less is known, however, about the distinguishing features of these enzymes, particularly those of the RNA-dependent RNA polymerase class. The 1. 9 A resolution crystal structure of hepatitis C virus (HCV) nonstructural protein 5B (NS5B) presented here provides the first complete and detailed view of an RNA-dependent RNA polymerase. While canonical polymerase features exist in the structure, NS5B adopts a unique shape due to extensive interactions between the fingers and thumb polymerase subdomains that serve to encircle the enzyme active site. Several insertions in the fingers subdomain account for intersubdomain linkages that include two extended loops and a pair of antiparallel alpha-helices. The HCV NS5B apoenzyme structure reported here can accommodate a template:primer duplex without global conformational changes, supporting the hypothesis that this structure is essentially preserved during the reaction pathway. This NS5B template:primer model also allows identification of a new structural motif involved in stabilizing the nascent base pair.

Publication types

  • Comparative Study

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Apoenzymes / chemistry
  • Base Pairing
  • Binding Sites
  • Conserved Sequence
  • Crystallization
  • Crystallography, X-Ray
  • HIV Reverse Transcriptase / chemistry
  • Hepacivirus / enzymology*
  • Hydrogen Bonding
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Structure, Secondary
  • RNA / chemistry
  • RNA / genetics
  • RNA / metabolism
  • RNA-Dependent RNA Polymerase / chemistry*
  • Recombinant Fusion Proteins / chemistry
  • Templates, Genetic
  • Viral Nonstructural Proteins / chemistry*


  • Apoenzymes
  • RNA primers
  • Recombinant Fusion Proteins
  • Viral Nonstructural Proteins
  • RNA
  • NS-5 protein, hepatitis C virus
  • RNA-Dependent RNA Polymerase
  • HIV Reverse Transcriptase

Associated data

  • PDB/1C2P