Mechanisms of ammonia activation and ammonium ion inhibition of quinoprotein methanol dehydrogenase: A computational approach

Abstract

The mechanism of methanol oxidation by quinoprotein methanol dehydrogenase (MDH·PQQ) in combination with methanol (MDH·PQQ·methanol) involves Glu-171 general base removal of the hydroxyl proton of methanol in concert with hydride equivalent transfer to the quinone carbon of pyrroloquinoline quinone (PQQ) and rearrangement to hydroquinone (PQQH₂) with release of formaldehyde. Molecular dynamics (MD) studies of the structures of MDH·PQQ·methanol in the presence of activator NH₃ and inhibitor have been carried out. In the MD structure of MDH·PQQ·methanol·NH₃, the hydrated NH₃ resides at a distance of ≈24 Å away from methanol and the ortho-quinone portion of PQQ. As such, influence of NH₃ on the oxidation reaction is not probable. We find that competes with the substrate by hydrogen-bonding to Glu-171 such that the complex is not reactive. Ammonia readily forms imines with quinone. Imines are present in solution as neutral () and protonated () species. MD simulations establish that the derivative of structure is unreactive because of the nonproductive means of methanol binding. The structure obtained by the MD simulations with the neutral imine of MDH·PQQ(NH)·methanol structure is similar to the reactive MDH·PQQ·methanol complex. This active site geometry allows for catalysis of hydride equivalent transfer to the of PQQ(NH) by concerted Glu-171 general-base removal of the HOCH₃ proton and Arg-324H⁺ general-acid proton transfer to the imine nitrogen. Enzyme-bound derivative of PQQ [PQQ(NH)] and CH₂O product are formed.