The Novel Two-Metal-Ion Mechanism for Type II Topoisomerases by the QM/MM and Free Energy Study

Catalysis of Type II topoisomerase employs a combination of nucleobase and divalent metal ions with a long discussing two-metal-ion mechanism. High-level quantum mechanics/molecular mechanics (QM/MM) and thermodynamics cycle perturbation (QTCP) free energy calculations support an associative novel two-metal-ion mechanism and elucidate the catalytic roles of metal ion, in which one divalent metal ion stabilizes the phosphoric pentacovalent transition state and the 3’‒OH leaving group while the secondary one facilitates to reorganize the nearby hydrogen network and residues. The DNA scission is fast and exothermic that a stepwise pathway proceeds for the nucleophilic attack by Y805 following by the protonation of the ribose alkoxide, inducing the formation of a bending DNA strand. These findings advance the fundamental knowledge on topoisomerases and the development of targeting anticancer drugs.