Figure 7.

Proposed scheme for DNA cleavage in the absence of divalent ions. The scheme is based on the structure of the MtbTOP1-704t/ssDNA complex (PDB 6CQI). The active site tyrosine Y342 hydroxyl group is positioned for attack of the scissile phosphate through the network of non-covalent interactions extending from the vicinity of Y342 to Y176 shown in Figures 1 and 2. A water nearby that is invisible in the PDB structure is required to act as general base (B:) to activate the hydroxyl nucleophile. The positive charge of the Arg344 side chain plays a critical role in stabilizing the negative charge on the hydroxyl nucleophile and the transition state. The E24 side chain interacts directly as general acid with the DNA 3′-hydroxyl leaving group to provide a proton that can be extracted from the positively charged H389 side chain via proton relay through the D111 side chain.