Abstract
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.
Highlights
Bacterial type II topoisomerases change the topological state of DNA for the initiation of DNA replication and decatenation of daughter chromosomal DNA at the end of replication [1,2,3,4].Bacteria express two highly similar type II topoisomerases, topoisomaerase IV and DNA gyrase.These enzymes introduce a transient break into one DNA segment (G segment) and pass anotherDNA segment (T segment) through the break, which is resealed [5,6]
We 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
Summary
Bacterial type II topoisomerases change the topological state of DNA for the initiation of DNA replication and decatenation of daughter chromosomal DNA at the end of replication [1,2,3,4].Bacteria express two highly similar type II topoisomerases, topoisomaerase IV and DNA gyrase.These enzymes introduce a transient break into one DNA segment (G segment) and pass anotherDNA segment (T segment) through the break, which is resealed [5,6]. Bacteria express two highly similar type II topoisomerases, topoisomaerase IV and DNA gyrase. These enzymes introduce a transient break into one DNA segment (G segment) and pass another. DNA segment (T segment) through the break, which is resealed [5,6]. The corresponding DNA gyrase subunits are named GyrA and GyrB [7]. They utilize the energy of ATP hydrolysis for their catalytic activity [8,9]. The transported T-segment DNA is trapped by ATP-dependent dimerization of the ATPase domains of ParE or GyrB before being presented to the cleavage site of the G-segment
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