Catalytic roles of coenzyme pyridoxal-5′-phosphate (plp) in plp-dependent enzymes: reaction pathway for methionine-γ-lyase-catalyzed l -methionine depletion

Pyridoxal-5′-phosphate (PLP), the active form of vitamin B₆, is an important and versatile coenzyme involved in a variety of enzymatic reactions, accounting for about 4% of all classified activities. However, the detailed catalytic reaction pathways for PLP-dependent enzymes remain to be explored. Methionine-γ-lyase (MGL), a promising alternative antitumor agent to conventional chemotherapies whose catalytic mechanism is highly desired for guiding further development of re-engineered enzymes, was used as a representative PLP-dependent enzyme, and the catalytic mechanism for l-Met elimination by MGL was explored at the first-principles quantum mechanical/molecular mechanical (QM/MM) level with umbrella sampling. The QM/MM calculations revealed that the enzymatic reaction pathway consists of 4 stages for a total of 19 reaction steps with five intermediates captured in available crystal structures. Furthermore, the more comprehensive role of PLP was revealed. Besides the commonly known role of "electron sink", coenzyme PLP can also assist proton transfer and temporarily store the excess proton generated in some intermediate states by using its hydroxyl group and phosphate group. Thus, PLP participated in most of the 19 steps. This study not only provided a theoretical basis for further development and re-engineering MGL as a potential antitumor agent but also revealed the comprehensive role of PLP which could be used to explore the mechanisms of other PLP-dependent enzymes.