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Polymerase β simulations suggest that Arg258 rotation is a slow step rather than large subdomain motionsper se11 Edited by B. Honig

Authors
Journal
Journal of Molecular Biology
0022-2836
Publisher
Elsevier
Publication Date
Volume
317
Issue
5
Identifiers
DOI: 10.1006/jmbi.2002.5450
Keywords
  • Regular Article
Disciplines
  • Biology

Abstract

Abstract The large-scale opening motion of mammalian DNA polymerase β is followed at atomic resolution by dynamic simulations that link crystal “closed” and “open” conformations. The closing/opening conformational change is thought to be key to the ability of polymerases to choose a correct nucleotide (through “induced fit”) and hence maintain DNA repair synthesis fidelity. Corroborating available structural and kinetic measurements, our studies bridge static microscopic crystal structures with macroscopic kinetic data by delineating a specific sequence, Phe272 ring flip, large thumb movement, Arg258 rotation with release of catalytic Mg 2+, together with estimated time-scales, that suggest the Arg258 rearrangement as a limiting factor of large subdomain motions. If similarly slow in the closing motion, this conformational change might be restricted further when an incorrect nucleotide binds and thus play a role in pol β’s selectivity for the correct nucleotide. These results suggest new lines of experimentation in the study of polymerase mechanisms (e.g. enzyme mutants), which should provide further insights into mechanisms of error discrimination and DNA synthesis fidelity.

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