Fig. 3

Modification of the transition-state theory. a The transition state theory suggests (1) a quasi-equilibrium between the substrate and transition state, which have the same chemical components, and (2) enzyme accelerating reaction rate by stabilizing transition state and thus reducing the energy barrier. The uncatalyzed and enzyme-catalyzed reaction processes are shown in grey and blue, respectively. We find that the canonical two Mg²⁺ ions are insufficient to support DNA synthesis. b Finding a third Mg²⁺ ion necessary for catalysis leads us to propose a new paradigm. The enzyme helps reaction substrates to capture the additional divalent cation and obtain necessary energy for transition from the substrate to product state