A model for the mechanism of strand passage by DNA gyrase

The mechanism of type II DNA topoisomerases involves the formation of an en zyme-operated gate in one double-stranded DNA segment and the passage of an other segment through this gate. DNA gyrase is the only type II topoisomera se able to introduce negative supercoils into DNA a feature that requires t he enzyme to dictate the directionality of strand passage. Although it is k nown that this is a consequence of the characteristic wrapping of DNA by gy rase, the detailed mechanism by which the transported DNA segment is captur ed 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 superhe lical density of the DNA substrate, setting up an equilibrium of the transp orted segment across the DNA gate. The overall efficiency of strand passage is determined by the position of this equilibrium, which depends on the su perhelical density of the DNA substrate. This mechanism is concerted, in th at capture of the transported segment by the ATP-operated clamp induces ope ning of the DNA. gate, which in turn stimulates ATP hydrolysis.