Crystal structure of a complex of a type IA DNA topoisomerase with a single-stranded DNA molecule

A variety of cellular processes, including DNA replication, transcription, and chromosome condensation, require enzymes that can regulate the ensuing topological changes occurring in DNA. Such enzymes-DNA topoisomerases-alter DNA topology by catalysing the cleavage of single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA), the passage of DNA through the resulting break , and the rejoining of the broken phosphodiester backbone(1). DNA topoisome rase III from Escherichia coli belongs to the type IA family of DNA topoiso merases, which transiently cleave ssDNA via formation of a covalent 5' phos photyrosine intermediate. Here we report the crystal structure, at 2.05 Ang strom resolution, of an inactive mutant of E. coli DNA topoisomerase III in a non-covalent complex with an 8-base ssDNA molecule. The enzyme undergoes a conformational change that allows the oligonucleotide to bind within a g roove leading to the active site. We note that the ssDNA molecule adopts a conformation like that of B-DNA while bound to the enzyme. The position of the DNA within the realigned active site provides insight into the role of several highly conserved residues during catalysis. These findings confirm various aspects of the type IA topoisomerase mechanism while suggesting fun ctional implications for other topoisomerases and proteins that perform DNA rearrangements.