W0311: DNA Interactions and Conformational Changes in Type IA DNA Topoisomerases

DNA topoisomerases are the enzymes responsible for controlling and maintaining the topological state of DNA. Type IA enzymes work by transiently breaking the phosphodiester backbone of one strand to allow passage of another strand through the break. The protein has to perform complex rearrangements of the DNA that may involve different DNA binding sites. In order to identify some of the DNA binding sites in the protein, we have solved the structures of several complexes of the 67 kDa amino terminal fragment of E. coli DNA topoisomerase I with nucleotides. The complexes show the presence of five different binding sites. Furthermore, it has been proposed that both type IA and type II topoisomerases change conformation dramatically during the reaction cycle in order to accomplish the DNA topological transformations. In the case of E. coli DNA topoisomerase I, it has been suggested that a 30 kDa fragment moves away from the rest of the protein to create an entrance into the central hole in the protein. Structures of the 30 kDa fragment reveal that indeed this fragment can change conformation significantly. The studies on DNA binding and conformational changes of DNA topoisomerase I allow us to propose refinements to our mechanism of action for type IA DNA topoisomerases.