A QM/MM MD study of the pH-dependent ring-opening catalysis and lid motif flexibility in glucosamine 6-phosphate deaminase

The glucosamine 6-phosphate deaminase (NagB), which catalyzes the conversion of D-glucosamine 6-phosphate (GlcN6P) into D-fructose 6-phosphate (F6P) and ammonia, determines the final metabolic fate of N-acetylglucosamine (GlcNAc). Here using state-of-the-art ab initio QM/MM MD simulations, we have explored the plausible mechanisms for the enzymatic ring-opening of GlcN6P in the basic environment. Two different proton-shuttle mechanisms have been proposed. Calculations show that the protonated state of the amino group in the substrate dominates the concerted and stepwise catalytic pathways and a catalytic triad plays an important role in mediating the proton transfer and the resulting ring-opening process. The free energy barrier for the rate-determining step in the low-energy stepwise reaction is 17.9 kcal mol−1. In acidic solution, the lid motif prefers a closed state while it always stays in the open state in basic solution upon substrate binding, which is basically dominated by the protonated state of the residue His145.