We have cloned and overexpressed a gene encoding a 43-kDa protein corresponding to the N-terminal fragment of the DNA gyrase B subunit. We show that this protein hydrolyzes ATP and binds coumarin drugs. The hydrolysis of ATP shows distinctly non-Michaelis-Menten kinetics and is consistent with a scheme in which the active form of the protein is a dimer, a conclusion supported by molecular weight studies. The coumarin drugs bind very tightly to the 43-kDa fragment, with novobiocin binding to the protein monomer and coumermycin A1 apparently inducing the formation of a dimer. The implications of these results with respect to the mechanism of supercoiling by DNA gyrase and the inhibition of gyrase by coumarin drugs are discussed.

We have characterized the interaction of a new class of antibiotics, simocyclinones, with bacterial DNA gyrase. Even though their structures include an aminocoumarin moiety, a key feature of novobiocin, coumermycin A 1 , and clorobiocin, which also target gyrase, simocyclinones behave strikingly differently from these compounds. Simocyclinone D8 is a potent inhibitor of gyrase supercoiling, with a 50% inhibitory concentration lower than that of novobiocin. However, it does not competitively inhibit the DNA-independent ATPase reaction of GyrB, which is characteristic of other aminocoumarins. Simocyclinone D8 also inhibits DNA relaxation by gyrase but does not stimulate cleavage complex formation, unlike quinolones, the other major class of gyrase inhibitors; instead, it abrogates both Ca 2؉ -and quinolone-induced cleavage complex formation. Binding studies suggest that simocyclinone D8 interacts with the N-terminal domain of GyrA. Taken together, our results demonstrate that simocyclinones inhibit an early step of the gyrase catalytic cycle by preventing binding of the enzyme to DNA. This is a novel mechanism for a gyrase inhibitor and presents new possibilities for antibacterial drug development.DNA topoisomerases are enzymes that control the topology of DNA in cells (5). The enzymes are divided into two types, topoisomerases I and II, depending on whether their reactions involve breakage of one or both strands of the DNA. Overall, the mechanism of action of topoisomerases involves the passage of one segment of DNA through a break in another. This reaction can achieve all the known reactions of topoisomerases: relaxation and supercoiling, catenation and decatenation, and knotting and unknotting. DNA supercoiling activity is unique to gyrase, and as this enzyme is essential in all bacteria but is not found in humans, it is an ideal target for antibacterials (24). The enzyme consists of an A 2 B 2 heterotetramer. The A subunit (GyrA; 97 kDa in Escherichia coli) comprises an N-terminal domain involved in DNA cleavage and religation and a C-terminal DNA-wrapping domain. The B subunit (GyrB; 90 kDa in E. coli) contains the site of ATP hydrolysis at the N-terminal domain (GyrB43); the C-terminal domain interacts with both GyrA and DNA. To introduce supercoils, the enzyme wraps a double-stranded segment around itself, cleaves this DNA (the gate segment) in both strands, passes the wrapped DNA (transported segment) through the break, and then reseals the DNA.DNA gyrase is a proven target for antibacterial agents (24). Two well-studied classes of drugs target the enzyme: the coumarins and the quinolones. Quinolones are synthetic compounds that are widely used in clinical practice (8). Coumarins are naturally occurring products of Streptomyces species which, despite being more potent inhibitors of gyrase in vitro than quinolones, have had limited clinical use due to their low solubility, poor uptake, and eukaryotic cell toxicity (27). Other gyrase inhibitors include the cyclothialidines and the bacterial toxins CcdB and m...

No abstract

No abstract