Fig. 5: Schematic representation of the hypothetical pathway for the hydrolysis reaction.
From: Molecular basis for the catalytic mechanism of human neutral sphingomyelinases 1 (hSMPD2)
a the reactant (R); (b) transition state (TS); (c) product (P) state along phosphodiester bond cleavage; The protons transferred during the reaction are colored with purple. K116 provides a proton (colored with cyan) to stabilize the P state; (d) free energy surface along the forming P-Onuc bond and the leaving group P-Olg bond. The insert indicates the free energy profile as a reaction coordinate of dr = r1-r2.
