TWO MODES OF DRUG BINDING Fluoroquinolone-Gyrase-DNA Complexes:

Background: X-ray crystal structures of fluoroquinolone-gyrase-DNA complexes reveal a single drug-binding mode. Results: A ciprofloxacin derivative with a chloroacetyl moiety at the C-7 end cross-linked with cysteine substitutions in both GyrA and GyrB that were 17 Å apart. Conclusion: Cleaved complexes containing gyrase have two fluoroquinolone-binding modes. Significance: The additional drug-binding mode provides new ways to investigate inhibitor-topoisomerase interactions. DNA gyrase and topoisomerase IV control bacterial DNA topology by breaking DNA, passing duplex DNA through the break, and then resealing the break. This process is subject to reversible corruption by fluoroquinolones, antibacterials that form drug-enzyme-DNA complexes in which the DNA is bro-ken. The complexes, called cleaved complexes because of the presence of DNA breaks, have been crystallized and found to have the fluoroquinolone C-7 ring system facing the GyrB/ParE subunits. As expected from x-ray crystallography, a thiol-reac-tive, C-7-modified chloroacetyl derivative of ciprofloxacin (Cip