His-172 and Tyr-169 are components of a triad in the active site of trimethylamine dehydrogenase (TMADH) comprising Asp-267, His-172, and Tyr-169, Stopped-flow kinetic studies with trimethylamine as substrate have indicated that mutation of His-172 to Gin reduces the limiting rate constant for flavin reduction similar to 10-fold (Basran, J,, Sutcliffe, M. J,, Hille, R,, and Scrutton, N, S, (1999) Biochem, J, 341, 397-314), A kinetic isotope effect (KIE = k(H)/K-D) accompanies flavin reduction by H172Q TIMADH, the magnitude of which varies significantly with solution pH, With trimethylamine, flavin reduction by H172Q TMADH is controlled by a single macroscopic ionization (pK(a) = 6.8 +/- 0.1), This ionization is perturbed (pK(a) = 7.4 +/- 0.1) in reactions with perdeuterated trimethylamine and is responsible for the apparent variation in the KIE with solution pH, At pH 9.5, where the functional group controlling flavin reduction is fully ionized, the KIE is independent of temperature in the range 277-297 K, consistent with vibrationally assisted hydrogen tunneling during breakage of the substrate C-H bond. Y169F TMADH is similar to4-fold more compromised than H172Q TMADH for hydrogen transfer, which occurs non-classically. Studies with Y169F TMADH suggest partial thermal excitation of substrate prior to hydrogen tunneling by a vibrationally assisted mechanism. Our studies illustrate the varied effects of compromising mutations on tunneling regimes in enzyme molecules.