A crystal structure of the bifunctional antibiotic simocyclinone D8, bound to DNA gyrase.
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.
Edwards
Marcus J
MJ
Department of Biological Chemistry, John Innes Centre, Colney, Norwich NR4 7UH, UK.
Flatman
Ruth H
RH
Mitchenall
Lesley A
LA
Stevenson
Clare E M
CE
Le
Tung B K
TB
Clarke
Thomas A
TA
McKay
Adam R
AR
Fiedler
Hans-Peter
HP
Buttner
Mark J
MJ
Lawson
David M
DM
Maxwell
Anthony
A
D000595:Amino Acid Sequence; D000900:Anti-Bacterial Agents / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology; D001665:Binding Sites; D003374:Coumarins / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology; D018360:Crystallography, X-Ray; D027081:DNA Gyrase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D004269:DNA, Bacterial / Q000378:metabolism; D024881:Drug Resistance, Bacterial; D004926:Escherichia coli / Q000187:drug effects / Q000201:enzymology* / Q000235:genetics; D006027:Glycosides / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D008970:Molecular Weight; D016297:Mutagenesis, Site-Directed; D009154:Mutation; D055503:Protein Multimerization; D017434:Protein Structure, Tertiary; D059005:Topoisomerase II Inhibitors
D000900:Anti-Bacterial Agents; D003374:Coumarins; D004269:DNA, Bacterial; D006027:Glycosides; D008024:Ligands; D059005:Topoisomerase II Inhibitors; C416814:simocyclinone D8; D027081:DNA Gyrase