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PMID: 12857958 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

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

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 100 ·No. 15 ·2003-07-22 ·Pages 8654-9

Stone MD, Bryant Z, Crisona NJ, Smith SB, Vologodskii A, Bustamante C, Cozzarelli NR

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.

MeSH Terms
DNA Replication DNA Topoisomerase IV/metabolism DNA, Bacterial/chemistry,metabolism DNA, Superhelical/chemistry,metabolism Escherichia coli/enzymology Models, Biological Models, Molecular Monte Carlo Method Nucleic Acid Conformation Stereoisomerism Thermodynamics
Chemicals
DNA, Bacterial DNA, Superhelical DNA Topoisomerase IV
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Stone Michael D
Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
Bryant Zev
Crisona Nancy J
Smith Steven B
Vologodskii Alexander
Bustamante Carlos
Cozzarelli Nicholas R
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Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.1133178100
Published
2003-07-22
Epub
2003-00-11
Pages
8654-9
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC166367
Subset
IM
External Links
PubMed source DOI: 10.1073/pnas.1133178100 PMC Full Text View journal details
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