Structure and conformational changes of DNA topoisomerase II visualized by electron microscopy

Type II DNA topoisomerases, which create a transient gate in duplex DNA and transfer a second duplex DNA through this gate, are essential for topological transformations of DNA in prokargotic and eukaryotic cells and are of interest not only from a mechanistic perspective but also because they are targets of agents for anticancer and antimicrobial chemotherapy. Here we describe the structure of the molecule of human topoisomerase II [DNA topoisomerase (ATP-hydrolyzing), EC 5.99.1.3] as seen by scanning transmission electron microscopy. A globular approximate to 90-Angstrom diameter core is connected by linkers to two approximate to 50-Angstrom domains, which were shown by comparison with genetically truncated Saccharomyces cerevisiae topoisomerase II to contain the N-terminal region of the approximate to 170-kDa subunits and that are seen in different orientations, When the ATP-binding site is occupied by a nonhydrolyzable ATP analog, a quite different structure is seen that results from a major conformational change and consists of two domains approximate to 90 Angstrom and approximate to 60 Angstrom in diameter connected by a linker, and in which the N-terminal domains have interacted. About two-thirds of the molecules show an approximate to 25-Angstrom tunnel in the apical part of the large domain, and the remainder contain an internal cavity approximate to 30 Angstrom wide in the large domain close to the linker region, We propose that structural rearrangements lead to this displacement of an internal tunnel. The tunnel is likely to represent the channel through which one DNA duplex, after capture in the clamp formed by the N-terminal domains, is transferred across the interface between the enzyme's subunits, These images are consistent with biochemical observations and provide a structural basis for understanding the reaction of topoisomerase II.