4CKL

Structure of 55 kDa N-terminal domain of E. coli DNA gyrase A subunit with simocyclinone D8 bound

Summary for 4CKL

• Entry DOI: 10.2210/pdb4ckl/pdb
• Related: 4CKK
• Descriptor: DNA GYRASE SUBUNIT A, SIMOCYCLINONE D8 (3 entities in total)
• Functional Keywords: isomerase, topoisomerase, antibiotic target
• Biological source: ESCHERICHIA COLI
• Cellular location: Cytoplasm (Potential): P0AES5
• Total number of polymer chains: 2
• Total formula weight: 111695.07

Authors

Hearnshaw, S.J.,Edwards, M.J.,Stevenson, C.E.M.,Lawson, D.M.,Maxwell, A. (deposition date: 2014-01-07, release date: 2014-03-12, Last modification date: 2023-12-20)

Primary citation

Hearnshaw, S.J.,Edwards, M.J.,Stevenson, C.E.,Lawson, D.M.,Maxwell, A.
A New Crystal Structure of the Bifunctional Antibiotic Simocyclinone D8 Bound to DNA Gyrase Gives Fresh Insight Into the Mechanism of Inhibition.
J.Mol.Biol., 426:2023-, 2014

PubMed Abstract: 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.

PubMed: 24594357
DOI: 10.1016/J.JMB.2014.02.017

Experimental method

X-RAY DIFFRACTION (2.05 Å)