Hammad Ali Hassan, Sadaf Rani, Farooq Ahmad Kiani, Stefen Fischer, Sohaib Aslam, Abeera Sikandar
Hydrolysis of phosphate containing compounds is the key chemical reaction in biology that requires the breaking of O–H bond of water and P–O bond of the substrate. Latest computations reveal two proton transfer modes from the attacking water to the phosphate containing substrate during hydrolysis, i.e., a) direct proton transfer, and b) proton relay via a mediating base. We point out that the hydrolysis mechanisms can be classified based on the sequence in which O–H and P–O bonds break, the strength of the leaving nucleophile, and the modes of proton transfer. This results into a scheme that can be used to understand two specialized catalytic strategies utilized by the enzymes to hydrolyze the P–O–X (X=P, C) linkages: 1) Enzymes lower the nucleophile strength of the leaving group to facilitate the breaking of the scissile P–Ol bond and shift one formal negative charge from phosphate reaction center to the leaving nucleophile. 2) Many enzymes avoid direct proton transfer from the attacking water molecule to the phosphate reaction center. The direct proton transfer puts an excess proton (positive charge) on the phosphate reaction center that hinders the breaking of the P–Ol bond between phosphate and the leaving nucleophile. On the contrary, the indirect proton transfer from attacking water to the phosphate reaction center via helping water or an assisting catalytic base does not hinder the P–Ol bond breaking. These two strategies are present in many phosphate hydrolyzing enzymes.