How a B family DNA polymerase has been evolved to copy RNA

Woo Suk Choi, Peng He, Arti Pothukuchy, Jimmy Gollihar, Andrew D. Ellington, Wei Yang

Research output: Contribution to journalArticle

Abstract

We report here crystal structures of a reverse transcriptase RTX, which was evolved in vitro from the B family polymerase KOD, in complex with either a DNA duplex or an RNA-DNA hybrid. Compared with the apo, binary, and ternary complex structures of the original KOD polymerase, the 16 substitutions that result in the function of copying RNA to DNA do not change the overall protein structure. Only six substitutions occur at the substrate-binding surface, and the others change domain-domain interfaces in the polymerase to enable RNA-DNA hybrid binding and reverse transcription. Most notably, F587L at the Palm and Thumb interface stabilizes the open and apo conformation of the Thumb. The intrinsically flexible Thumb domain seems to play a major role in accommodating the RNA-DNA hybrid product distal to the active site. This is reminiscent of naturally occurring RNA-dependent DNA polymerases, including telomerase, which have a dramatically augmented Thumb domain, and of reverse transcriptase, which extends its Thumb with the RNase H domain.

Original languageEnglish (US)
Pages (from-to)21274-21280
Number of pages7
JournalProceedings of the National Academy of Sciences of the United States of America
Volume117
Issue number35
DOIs
StatePublished - Sep 1 2020

Keywords

  • 3' to 5' exonuclease
  • Proofreading
  • Reverse transcription
  • Thumb domain

ASJC Scopus subject areas

  • General

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