Due
to the recent surge in antibiotic resistance, developing
novel
antibiotics is the demand of the time, and thus, a precise understanding
of the catalytic mechanisms of enzymes involved in antibiotic biosynthesis
becomes crucial. Here, we present a comprehensive investigation into
the catalytic mechanism of TokK, a freshly characterized B12-dependent RSMT enzyme that plays an important role in carbapenem
biosynthesis. Using MD simulations, we show how the plasticity of
the active site facilitates substrate recognition while the quantum
mechanics/molecular mechanics calculations provide a detailed mechanistic
understanding of the methyl transfer process, elucidating stereochemical
preferences. Notably, we demonstrate the indispensable role of Trp215
in orchestrating the proper orientation of the 5′-dA• radical for efficient substrate methylation, which strongly correlates
with the previous findings where the mutation of Trp215 has severely
affected the enzyme activity.