Stringent control of the RNA-dependent RNA polymerase translocation revealed by multiple intermediate structures

Nat Commun. 2020 May 25;11(1):2605. doi: 10.1038/s41467-020-16234-4.

Abstract

Each polymerase nucleotide addition cycle is associated with two primary conformational changes of the catalytic complex: the pre-chemistry active site closure and post-chemistry translocation. While active site closure is well interpreted by numerous crystallographic snapshots, translocation intermediates are rarely captured. Here we report three types of intermediate structures in an RNA-dependent RNA polymerase (RdRP). The first two types, captured in forward and reverse translocation events, both highlight the role of RdRP-unique motif G in restricting the RNA template movement, corresponding to the rate-limiting step in translocation. By mutating two critical residues in motif G, we obtain the third type of intermediates that may mimic the transition state of this rate-limiting step, demonstrating a previously unidentified movement of the template strand. We propose that a similar strategy may be utilized by other classes of nucleic acid polymerases to ensure templating nucleotide positioning for efficient catalysis through restricting interactions with template RNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Amino Acid Substitution
  • Base Sequence
  • Biological Transport, Active
  • Catalytic Domain
  • Crystallography, X-Ray
  • Enterovirus A, Human / enzymology
  • Enterovirus A, Human / genetics
  • Genes, Viral
  • Humans
  • Models, Molecular
  • Mutagenesis, Site-Directed
  • Nucleic Acid Conformation
  • Protein Conformation
  • RNA, Viral / chemistry
  • RNA, Viral / genetics
  • RNA, Viral / metabolism
  • RNA-Dependent RNA Polymerase / chemistry*
  • RNA-Dependent RNA Polymerase / genetics
  • RNA-Dependent RNA Polymerase / metabolism*
  • Transcription Elongation, Genetic
  • Viral Proteins / chemistry
  • Viral Proteins / genetics
  • Viral Proteins / metabolism

Substances

  • RNA, Viral
  • Viral Proteins
  • RNA-Dependent RNA Polymerase