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Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerases.

Authors
  • Michael Stone
  • Z, Bryant
  • Nj, Crisona
  • Sb, Smith
  • A, Vologodskii
  • C, Bustamante
  • Nr, Cozzarelli
Type
Published Article
Journal
Proceedings of the National Academy of Sciences
Publisher
Proceedings of the National Academy of Sciences
Volume
100
Issue
15
Pages
8654–8659
Source
UCSC Cancer biomedical-ucsc
License
Unknown

Abstract

Escherichia coli topoisomerase (Topo) IV is an essential type II Topo that removes DNA entanglements created during DNA replication. Topo IV relaxes (+) supercoils much faster than (-) supercoils, promoting replication while sparing the essential (-) supercoils. Here, we investigate the mechanism underlying this chiral preference. Using DNA binding assays and a single-molecule DNA braiding system, we show that Topo IV recognizes the chiral crossings imposed by the left-handed superhelix of a (+) supercoiled DNA, rather than global topology, twist deformation, or local writhe. Monte Carlo simulations of braid, supercoil, and catenane configurations demonstrate how a preference for a single-crossing geometry during strand passage can allow Topo IV to perform its physiological functions. Single-enzyme braid relaxation experiments also provide a direct measure of the processivity of the enzyme and offer insight into its mechanochemical cycle.

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