Theoretical Study On The Catalytic Mechanism Of Acetolactate Decarboxylase By QM/MM

Acetolactate decarboxylase [EC 4.1.1.5](ALDC) catalyze both decarboxylation/protonation of the natural substrate and the rearrangement of the non-natural substrate, which is an interesting phenomenon in biological systems. It is a metalloenzyme which converts natural substrate(S)-acetolactate to(R)-acetoin by decarboxylation and subsequent protonation. For the enantiomer(R)-acetolactate, ALDC does not directly proceed decarboxylation to make(R)-acetoin, it has to carry out a previous rearrangement reaction to produce(S)-acetolactate. Formerly, due to the lack of detail information of enzyme structure, we could not achieve what are the binding modes of the two enantiomers and how amino acids and zinc ion affect the rearrangement and decarboxylation. Recently, crystallized out of the ALDC’s structures, developed computer technology and quantum mechanics help us to speculate the reaction mechanism. In this study, a hybrid quantum mechanical/molecular mechanical(QM/MM) method at the ONIOM level was used to elicit the details of the catalytic mechanism and energy profiles along the reaction in atomic level. In the rearrangement process, the hydrogen bond between Glu253 and carboxyl of(R)-acetolactate is crucial when the carboxyl rearranges to adjacent carbonyl carbon to form(S)-acetolactate. In the decarboxylation process, ALDC catalyzes(S)-acetolactate by a two-step reaction. The first step is the carboxyl departure with forming enediol intermediate and carbon dioxide. The next step is the protonation reaction on the face opposite enediol intermediate. The calculations show that protonation reaction with waterassisted is more favorable than without water-assisted. And the protonation reaction is the rate-limiting step of the decarboxylation process. This study may help us to understand ALDC catalyzing R/S-acetolactate and similar stereoselective catalytic mechanism in biological systems.