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Crystal structure of the breakage–reunion domain of DNA gyrase

Abstract

DNA gyrase is a type II DNA topoisomerase from bacteria that introduces supercoils into DNA1,2. It catalyses the breakage of a DNA duplex (the G segment), the passage of another segment (the T segment) through the break, and then the reunification of the break. This activity involves the opening and closing of a series of molecular ‘gates’ which is coupled to ATP hydrolysis. Here we present the crystal structure of the ‘breakage–reunion’ domain of the gyrase at 2.8 Å resolution. Comparison of the structure of this 59K (relative molecular mass, 59,000) domain with that of a 92K fragment of yeast topoisomerase II (ref. 3) reveals a very different quaternary organization, and we propose that the two structures represent two principal conformations that participate in the enzymatic pathway. The gyrase structure reveals a new dimer contact with a grooved concave surface for binding the G segment and a cluster of conserved charged residues surrounding the active-site tyrosines. It also shows how breakage of the G segment can occur and, together with the topoisomerase II structure, suggests a pathway by which the T segment can be released through the second gate of the enzyme. Mutations that confer resistance to the quinolone antibacterial agents cluster at the new dimer interface, indicating how these drugs might interact with the gyrase–DNA complex.

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Figure 1: a, Domain organization of E.coli gyrase and yeast topoisomerase II.
Figure 2: a, b, Orthogonal views of GyrA59 and the yeast topo II A′ subunit.
Figure 3: a, GRASP22 electrostatic surface potential of the GyrA59 dimer (orthogonal stereo views).: negatively charged surfaces are in red, positively charged surfaces in blue.

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Acknowledgements

We thank C. Petosa, S. Kampranis, L. Bankston and M. Sutcliffe for discussion. We acknowledge the EMBL Hamburg outstation c/o DESY and the SRS in Daresbury for access to their faciities. This work was supported by the BBSRC. A.M. is a Lister Institute Jenner Fellow.

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  1. Correspondence and requests for materials should be addressed to R.C.L. Coordinates have been deposited with the Protein DataBank (1AB4).

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    Correspondence to Robert C. Liddington.

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    Cabral, J., Jackson, A., Smith, C. et al. Crystal structure of the breakage–reunion domain of DNA gyrase. Nature 388, 903–906 (1997). https://doi.org/10.1038/42294

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