The Catalytic Mechanism of Acetoacetate Decarboxylase: A Detailed Study of Schiff Base Formation, Protonation States, and Their Impact on Catalysis

The enzyme acetoacetate decarboxylase (AAD) has a crucial function in the process of decarboxylating the substrate acetoacetate (AA). It has been extensively studied over the years, but its exact catalytic mechanism has remained partly unsolved due to the difficulty in assessing reaction intermediates. In this study, we combine molecular dynamics and electronic structure calculations to rediscover its catalytic mechanism. Our results show that the presence of the substrate, the acetoacetate, significantly influences the electrostatic potential of the active site. Furthermore, our simulations show that the decarboxylation reaction can take place by means of a direct proton transfer instead of via an enamine intermediate, which is thought to be strictly necessary. This work provides new insights into the role of the electrostatic interactions on the catalytic activity of AAD and for the first time connects it to the catalytic mechanism of other decarboxylases.