TY - JOUR

T1 - A model for the mechanism of strand passage by DNA gyrase

AU - Kampranis, S C

AU - Bates, A D

AU - Maxwell, A

PY - 1999/7/20

Y1 - 1999/7/20

N2 - The mechanism of type II DNA topoisomerases involves the formation of an enzyme-operated gate in one double-stranded DNA segment and the passage of another segment through this gate. DNA gyrase is the only type II topoisomerase able to introduce negative supercoils into DNA, a feature that requires the enzyme to dictate the directionality of strand passage. Although it is known that this is a consequence of the characteristic wrapping of DNA by gyrase, the detailed mechanism by which the transported DNA segment is captured and directed through the DNA gate is largely unknown. We have addressed this mechanism by probing the topology of the bound DNA segment at distinct steps of the catalytic cycle. We propose a model in which gyrase captures a contiguous DNA segment with high probability, irrespective of the superhelical density of the DNA substrate, setting up an equilibrium of the transported segment across the DNA gate. The overall efficiency of strand passage is determined by the position of this equilibrium, which depends on the superhelical density of the DNA substrate. This mechanism is concerted, in that capture of the transported segment by the ATP-operated clamp induces opening of the DNA gate, which in turn stimulates ATP hydrolysis.

AB - The mechanism of type II DNA topoisomerases involves the formation of an enzyme-operated gate in one double-stranded DNA segment and the passage of another segment through this gate. DNA gyrase is the only type II topoisomerase able to introduce negative supercoils into DNA, a feature that requires the enzyme to dictate the directionality of strand passage. Although it is known that this is a consequence of the characteristic wrapping of DNA by gyrase, the detailed mechanism by which the transported DNA segment is captured and directed through the DNA gate is largely unknown. We have addressed this mechanism by probing the topology of the bound DNA segment at distinct steps of the catalytic cycle. We propose a model in which gyrase captures a contiguous DNA segment with high probability, irrespective of the superhelical density of the DNA substrate, setting up an equilibrium of the transported segment across the DNA gate. The overall efficiency of strand passage is determined by the position of this equilibrium, which depends on the superhelical density of the DNA substrate. This mechanism is concerted, in that capture of the transported segment by the ATP-operated clamp induces opening of the DNA gate, which in turn stimulates ATP hydrolysis.

KW - Adenosine Triphosphatases

KW - Adenosine Triphosphate

KW - Binding Sites

KW - DNA

KW - DNA Topoisomerases, Type I

KW - DNA Topoisomerases, Type II

KW - DNA, Superhelical

KW - Escherichia coli

KW - Models, Molecular

KW - Mutation

KW - Nucleic Acid Conformation

KW - Protein Conformation

M3 - Journal article

C2 - 10411889

VL - 96

SP - 8414

EP - 8419

JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

SN - 0027-8424

IS - 15

ER -