The functional domain structure of human DNA topoisomerase II␣ and Saccharomyces cerevisiae DNA topoisomerase II was studied by investigating the abilities of insertion and deletion mutant enzymes to support mitotic growth and catalyze transitions in DNA topology in vitro. Alignment of the human topoisomerase II␣ and S. cerevisiae topoisomerase II sequences defined 13 conserved regions separated by less conserved or differently spaced sequences. The spatial tolerance of the spacer regions was addressed by insertion of linkers. The importance of the conserved regions was assessed through deletion of individual domains. We found that the exact spacing between most of the conserved domains is noncritical, as insertions in the spacer regions were tolerated with no influence on complementation ability. All conserved domains, however, are essential for sustained mitotic growth of S. cerevisiae and for enzymatic activity in vitro. A series of topoisomerase II carboxy-terminal truncations were investigated with respect to the ability to support viability, cellular localization, and enzymatic properties. The analysis showed that the divergent carboxy-terminal region of human topoisomerase II␣ is dispensable for catalytic activity but contains elements that specifically locate the protein to the nucleus.Eukaryotic DNA topoisomerase II is an abundant nuclear enzyme involved in regulating the conversion of DNA between different topological isoforms (42, 60). It fulfills essential functions in DNA replication (41, 53) and chromosome segregation during both mitosis (26, 27) and meiosis (46), and it is thought to play a key role in certain types of DNA recombination events (8,10,22,30,48). The enzyme has furthermore been suggested to constitute a component of nuclear scaffold structures (3, 23), where it may be involved in chromosome condensation (4, 58) and decondensation (45).Topoisomerase II binds to DNA as a dimer and cleaves its DNA substrate with a 4-bp stagger (40, 60) at sites with loosely defined sequences (54). Upon DNA cleavage, each subunit of topoisomerase II becomes transiently ligated to the 5Ј ends of the respective DNA strands through an O 4 -phosphotyrosine bond involving a tyrosine residue in the active site of the protein (7, 36). Catalytic activity is ATP dependent, and it is performed by passing one intact DNA helix through the enzyme-mediated double-stranded DNA break, followed by rejoining of the DNA strands (42).Although the mechanics of topoisomerase II function have been characterized in great detail, little information has emerged about the functional organization of the enzyme. Proteolysis studies on purified topoisomerase II from Saccharomyces cerevisiae (35), Schizosaccharomyces pombe (50), Drosophila melanogaster (34), and humans (9) suggest that the enzyme is composed of three major structural domains, of which two are constituted by the conserved N-terminal and central parts of the protein and a third is constituted by the highly divergent C-terminal region.The fragment originating from the N-...