Motif D of viral RNA-dependent RNA polymerases determines efficiency and fidelity of nucleotide addition

Xiaorong Yang, Eric D. Smidansky, Kenneth R. Maksimchuk, David Lum, Jesse L. Welch, Jamie J. Arnold, Craig E. Cameron, David D. Boehr

Research output: Contribution to journalArticlepeer-review

62 Scopus citations

Abstract

Fast, accurate nucleotide incorporation by polymerases facilitates expression and maintenance of genomes. Many polymerases use conformational dynamics of a conserved α helix to permit efficient nucleotide addition only when the correct nucleotide substrate is bound. This α helix is missing in structures of RNA-dependent RNA polymerases (RdRps) and RTs. Here, we use solution-state nuclear magnetic resonance to demonstrate that the conformation of conserved structural motif D of an RdRp is linked to the nature (correct versus incorrect) of the bound nucleotide and the protonation state of a conserved, motif-D lysine. Structural data also reveal the inability of motif D to achieve its optimal conformation after incorporation of an incorrect nucleotide. Functional data are consistent with the conformational change of motif D becoming rate limiting during and after nucleotide misincorporation. We conclude that motif D of RdRps and, by inference, RTs is the functional equivalent to the fidelity helix of other polymerases.

Original languageEnglish (US)
Pages (from-to)1519-1527
Number of pages9
JournalStructure
Volume20
Issue number9
DOIs
StatePublished - Sep 5 2012

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology

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