Abstract
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.
| Original language | English |
|---|---|
| Journal | Proceedings of the National Academy of Sciences of the United States of America |
| Volume | 96 |
| Issue number | 15 |
| Pages (from-to) | 8414-9 |
| Number of pages | 6 |
| ISSN | 0027-8424 |
| Publication status | Published - 20 Jul 1999 |
Keywords
- Adenosine Triphosphatases
- Adenosine Triphosphate
- Binding Sites
- DNA
- DNA Topoisomerases, Type I
- DNA Topoisomerases, Type II
- DNA, Superhelical
- Escherichia coli
- Models, Molecular
- Mutation
- Nucleic Acid Conformation
- Protein Conformation