A New Crystal Structure of the Bifunctional Antibiotic Simocyclinone D8 Bound to DNA Gyrase Gives Fresh Insight into the Mechanism of Inhibition
| Autor: | David M. Lawson, Marcus J. Edwards, Anthony Maxwell, Stephen J. Hearnshaw, Clare E. M. Stevenson |
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| Rok vydání: | 2014 |
| Předmět: |
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Molecular Stereochemistry Dimer Plasma protein binding Isomerase Biology Crystallography X-Ray medicine.disease_cause DNA gyrase Article Protein Structure Secondary antibiotics 03 medical and health sciences chemistry.chemical_compound Tetramer Coumarins Structural Biology Drug Resistance Bacterial Escherichia coli medicine Topoisomerase II Inhibitors Glycosides Protein Structure Quaternary Molecular Biology DNA topoisomerase ASU asymmetric unit X-ray crystallography 030304 developmental biology 0303 health sciences EDTA ethylenediaminetetraacetic acid ITC isothermal titration calorimetry 030306 microbiology Isothermal titration calorimetry biochemical phenomena metabolism and nutrition SD8 simocyclinone D8 Anti-Bacterial Agents Protein Structure Tertiary 3. Good health Crystallography Amino Acid Substitution simocyclinones chemistry Protein Multimerization Topoisomerase-II Inhibitor Protein Binding |
| Zdroj: | Journal of Molecular Biology |
| ISSN: | 0022-2836 |
| DOI: | 10.1016/j.jmb.2014.02.017 |
| Popis: | Simocyclinone D8 (SD8) is an antibiotic produced by Streptomyces antibioticus that targets DNA gyrase. A previous structure of SD8 complexed with the N-terminal domain of the DNA gyrase A protein (GyrA) suggested that four SD8 molecules stabilized a tetramer of the protein; subsequent mass spectrometry experiments suggested that a protein dimer with two symmetry-related SD8s was more likely. This work describes the structures of a further truncated form of the GyrA N-terminal domain fragment with and without SD8 bound. The structure with SD8 has the two SD8 molecules bound within the same GyrA dimer. This new structure is entirely consistent with the mutations in GyrA that confer SD8 resistance and, by comparison with a new apo structure of the GyrA N-terminal domain, reveals the likely conformation changes that occur upon SD8 binding and the detailed mechanism of SD8 inhibition of gyrase. Isothermal titration calorimetry experiments are consistent with the crystallography results and further suggest that a previously observed complex between SD8 and GyrB is ~ 1000-fold weaker than the interaction with GyrA. Graphical abstract Highlights • Fragment engineered to reveal biologically relevant structure of GyrA–drug complex. • This structure fully explains all available biochemical/biophysical/genetic data. • Binding site in GyrB is ~ 1000-fold weaker than site in GyrA. |
| Databáze: | OpenAIRE |
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