Abstract: Type II topoisomerases have been the subject of intense biochemical and structural investigation since their discovery over three decades ago. These enzymes are necessary for all DNA-based life, since they provide a means to resolve the topological problems associated with long double-stranded DNAs: knotting, catenation, and supercoiling. Type II topoisomerases are dimeric enzymes with separate domains for DNA binding and cleavage, and ATP binding and hydrolysis. They act by capturing two double-stranded DNA segments, cleaving both strands of one segment, and passing the other segment through this break with high directional specificity, then resealing the first strand and releasing both strands. This dissertation outlines structural and biochemical investigations of several aspects of type II topoisomerase mechanisms. The second chapter shows that, despite overall architectural differences, the type IIB topoisomerases, found only in archaea and recently in some plants, share a similar ATPase region with the type IIA topoisomerases from eukarya and bacteria. In chapter 3, I structurally outline the ATP hydrolysis mechanism of a type IIB topoisomerase, and combine my results with prior biochemical findings to propose that ATP binding and hydrolysis does not directly power DNA strand passage: instead, the sequence of ATP binding, hydrolysis, and release dictates the order and timing of a sequence of conformational changes resulting in the passage of one DNA segment through another. In chapters 4 and 5, I outline the structures of unique DNA-binding domains in the bacterial type IIA topoisomerases DNA gyrase and topo IV In addition to identifying a new protein fold (the 'β-pinwheel'), my structural and biochemical studies show how these domains are responsible for the unique activities of DNA gyrase and topo IV. Overall, the work presented here strives to provide a clearer picture of the structures and physical mechanisms of type II topoisomerases, while synthesizing present work with prior biochemical findings. Increasingly, this picture is beginning to include not just the structures of the enzymes themselves, but also the active roles that ATP and DNA substrates play in the strand passage reaction.