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Crystal Structures of the 43 kDa ATPase Domain of Xanthomonas Oryzae pv. Oryzae Topoisomerase IV ParE Subunit and its Complex with Novobiocin

Department of Chemistry, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
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Crystals 2019, 9(11), 577; https://doi.org/10.3390/cryst9110577
Received: 29 October 2019 / Revised: 2 November 2019 / Accepted: 4 November 2019 / Published: 5 November 2019
(This article belongs to the Special Issue Crystallographic Studies of Enzymes)
Topoisomerase IV, one of the best-established antibacterial targets, is an enzyme crucial for chromosome segregation and cell division by catalyzing changes in DNA topology through breaking and rejoining DNA. This enzyme functions as a heterotetramer consisting of two ParC and two ParE subunits. Aminocoumarin class inhibitors target the ParE subunit, while widely used quinolones target the ParC subunit. Here, we determined the crystal structure of the ParE 43 kDa ATPase domain from Xanthomonas oryzae pv. oryzae. Size exclusion chromatography showed that the ParE ATPase domain exists as a monomer in solution, while it dimerizes when ATP is added. Structural comparison with the structure of Escherichia coli ParE in complex with an ATP analogue showed large conformational change of the subdomains within the protein. We also determined the structure of the ParE ATPase domain in complex with novobiocin, a natural product aminocoumarin class inhibitor, revealing its binding mode and the structural change within the ATP-binding site induced by novobiocin binding. These results could provide a basis for the design of more potent topoisomerase IV inhibitors with improved antibacterial activity. View Full-Text
Keywords: crystal structure; bacterial type II topoisomerase; topoisomerase IV; ParE; novobiocin crystal structure; bacterial type II topoisomerase; topoisomerase IV; ParE; novobiocin
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MDPI and ACS Style

Jung, H.Y.; Heo, Y.-S. Crystal Structures of the 43 kDa ATPase Domain of Xanthomonas Oryzae pv. Oryzae Topoisomerase IV ParE Subunit and its Complex with Novobiocin. Crystals 2019, 9, 577.

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