Abstract
Simocyclinones are bifunctional antibiotics that inhibit bacterial DNA gyrase by preventing DNA binding to the enzyme. We report the crystal structure of the complex formed between the N-terminal domain of the Escherichia coli gyrase A subunit and simocyclinone D8, revealing two binding pockets that separately accommodate the aminocoumarin and polyketide moieties of the antibiotic. These are close to, but distinct from, the quinolone-binding site, consistent with our observations that several mutations in this region confer resistance to both agents. Biochemical studies show that the individual moieties of simocyclinone D8 are comparatively weak inhibitors of gyrase relative to the parent compound, but their combination generates a more potent inhibitor. Our results should facilitate the design of drug molecules that target these unexploited binding pockets.
Publication types
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Research Support, Non-U.S. Gov't
MeSH terms
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Amino Acid Sequence
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Anti-Bacterial Agents / chemistry
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Anti-Bacterial Agents / metabolism
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Anti-Bacterial Agents / pharmacology
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Binding Sites
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Coumarins / chemistry
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Coumarins / metabolism
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Coumarins / pharmacology
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Crystallography, X-Ray
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DNA Gyrase / chemistry*
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DNA Gyrase / genetics
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DNA Gyrase / metabolism*
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DNA, Bacterial / metabolism
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Drug Resistance, Bacterial
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Escherichia coli / drug effects
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Escherichia coli / enzymology*
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Escherichia coli / genetics
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Glycosides / chemistry
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Glycosides / metabolism
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Glycosides / pharmacology
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Ligands
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Models, Molecular
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Molecular Sequence Data
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Molecular Weight
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Mutagenesis, Site-Directed
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Mutation
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Protein Multimerization
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Protein Structure, Tertiary
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Topoisomerase II Inhibitors
Substances
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Anti-Bacterial Agents
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Coumarins
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DNA, Bacterial
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Glycosides
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Ligands
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Topoisomerase II Inhibitors
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simocyclinone D8
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DNA Gyrase