We have purified human topoisomerase II␣ from HeLa cells and studied its ATPase reaction. The ATPase activity is stimulated by DNA and shows apparent MichaelisMenten kinetics. Although the ATPase activity of human topoisomerase II␣ is lower than that of Saccharomyces cerevisiae, it is more active in decatenation, implying more efficient coupling of the ATPase to DNA strand passage under these conditions. Using plasmid pBR322 as the DNA cofactor, the reaction shows hyperstimulation by DNA at a base pair to enzyme dimer ratio of 100 -200:1. When DNA fragments are used as the cofactor, the reaction requires >ϳ ϳ100 base pairs to stimulate the activity and fragments of ϳ ϳ300 base pairs show hyperstimulation. This behavior can be rationalized in terms of the enzyme requiring fragments that can bind to both the DNA gate and the ATP-operated clamp in order for the ATPase reaction to be stimulated. Hyperstimulation is a consequence of the saturation of DNA with enzyme. The mechanistic implications of these results are discussed.DNA topoisomerases are enzymes that catalyze topological changes in DNA (1, 2). These enzymes have been found in all cell types and are essential for cell viability. Their roles include maintenance of the level of intracellular DNA supercoiling, removing supercoils, which build up ahead of and behind transcription and replication complexes, and the decatenation of daughter chromosomes following replication. The topoisomerase reaction involves the breakage of DNA in one or both strands, the formation of protein-DNA covalent bonds, and the passage of another segment of DNA through the enzyme-stabilized break. In the case of type II enzymes, this DNA strand passage reaction generally requires the hydrolysis of ATP.As a consequence of their essential roles in cells, DNA topoisomerases have become important drug targets. For example, the prokaryotic type II enzyme DNA gyrase is the target of a range of antibacterial agents such as the quinolone and coumarin drugs (3). The eukaryotic type I enzyme, DNA topoisomerase I, is the target of the antitumor agent camptothecin, and eukaryotic topoisomerase II is the target of a variety of antitumor drugs, which include amsacrine, epipodophyllotoxins, and merbarone (4, 5). Many of these compounds (e.g. quinolones, camptothecin, amsacrine, etc.) act by stabilizing a cleavable complex between the topoisomerase and DNA, in which the enzyme is covalently linked to the DNA. Arresting of DNA replication forks by this complex is thought to initiate events that lead to cell death (5). Other topoisomerase-targeted compounds act by different mechanisms, e.g. coumarin drugs (such as novobiocin) act as competitive inhibitors of the DNA gyrase ATPase reaction (6) and ICRF-159 is thought to stabilize the eukaryotic enzyme in a closed complex incapable of catalytic activity (7).On the basis of the alignment of their amino acid sequences, DNA topoisomerases can be grouped into three subfamilies: type IA, type IB, and type II (8). All type II enzymes are evolutionarily and stru...