Mechanism and Catalytic Site Atlas

DNA topoisomerase enzymes modify DNA super-helicity and perform DNA decatenation using scission, manipulation and ligation reactions. Two families of topoisomerases exist, group I and II, cleaving single and double stranded DNA respectively. Each family can be subdivided into A and B groups, which represent subsets of proteins with no similarity in structure or sequence. All topoisomerases use a tyrosine to cleave DNA, forming a short-lived phosphotyrosyl intermediate. These bacterial enzymes reduce the topological stress in the DNA structure by relaxing negatively, but not positively, supercoiled DNA. Different classes of enzyme relax DNA to different extents and, for the 1A enzymes, activity correlates with the degree of DNA substrate superhelicity.

Type I DNA topoisomerase enzymes alter the topology of DNA by transiently breaking one or two strands of DNA, passing a single or double strand through the break and then resealing the break. This allows for the interconversion of topological isomers, which is necessary for a number of cellular transactions such as replication, transcription and recombination. The enzyme is a member of the IA sub family, classified by the covalently bound enzyme-DNA intermediate.

Unlike group II enzymes, the reactions catalysed by Escherichia coli topoisomerase are not coupled to binding or hydrolysis of ATP. Full-length topoisomerase I from Escherichia coli is a 97kDa metalloprotein containing three Zn(II) cations at the C-terminus. The structure annotated is a 67kDa, N-terminal truncation protein. While the tetra-cysteine motifs, thought to bind Zn(II) are not required for single strand DNA cleavage, without them the protein cannot relax negatively supercoiled DNA. However, the substrate specificity and reaction characteristics of the N-terminal truncation fragment are thought to parallel the full length and Zn depleted enzyme.