Structural and mechanistic analysis of type II DNA topoisomerases

DNA topoisomerases are essential enzymes that occur across all domains of life, involved in regulating DNA topology to facilitate essential processes like DNA replication, chromosome segregation and transcription. This function is based on their ability to establish transient DNA breaks and catalyse the passage of another DNA segment through the break before religation. How this process occurs is not well-understood, but the enzymes have become key targets for antibacterial and anti-cancer chemotherapy. Topoisomerase-targeted drugs work by disrupting the DNA cleavage-religation process. Here we will use biochemical and structural approaches to investigate this problem. A key issue will be the role of divalent cations (generally Mg2+) in DNA breakage-reunion. Many DNA nucleases are known to utilise Mg2+ to catalyse cleavage, but topoisomerases are able to combine cleavage and ligation in a coordinated manner to allow DNA passage without leaving a permanent break; exactly how this occurs is not clear. Recent biochemical and structural evidence suggests there are two Mg2+-binding sites per DNA strand on the enzyme. However, the precise mechanism, its regulation and its dynamics are poorly understood. Notably it is unclear whether two metal ions must bind at the same time or one metal can move between sites to catalyse cleavage/religation in a regulated manner. Recent structural/biochemical advances now present us with the opportunity to address questions surrounding the role of metals in cleavage-religation. The principles we derive will be applicable to many enzymes that utilise metals in this way, and will help with the development of antibacterial and anti-cancer drugs. The main approaches will be structural biology (X-ray crystallography) and enzymology.