Fig. 2: Mechanism and structure of type IIA topoisomerases.

a Proposed catalytic cycle of a type II topoisomerase illustrated for topo IV. The transported T-segment DNA (see stage 1) is captured by closure of the N-gate formed by ATP-induced dimerisation of the ParE ATPase domains (red) which allows its presentation to the cleavage core of the enzyme (2), passage through the G-segment DNA bound at the DNA cleavage gate (3) and subsequent release through the protein C-gate (4). Hydrolysis of bound ATP (pink dots) resets the enzyme for another cycle. The breakage-reunion (ParC55) and C-terminal domain (CTD) of ParC are in blue and silver; the TOPRIM domain of ParE (ParE30) is in yellow. G-gate DNA and transported (T) segment DNA are shown in green and purple, respectively. Bound ATP is shown by pink circles (Reproduced with permission under a Creative Commons licence from Fig. 1 of Laponogov, I et al., Nucleic Acids Res, 41, 9911-9923 (2013). Complexes 1, 2 and 3 (either with or lacking the ATPase domains and CTDs as in the core complex) can be captured as a cleavage complex by fluoroquinolones. b Domain organisation for the fused ParE-ParC cleavage core of S. pneumoniae topo IV (top) shown with that of the corresponding full-length ParE and ParC subunits (bottom). The open triangle shows the location of a potassium ion binding motif. c 18-mer E-site (E18) and V-site (V18) DNA duplexes are strongly cleaved (arrows) by S. pneumoniae topo IV in the presence of quinolones generating a 4 bp overhang (underlined).