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Both Chemical and Non-Chemical Steps Limit the Catalytic Efficiency of Family 4 Glycoside Hydrolases

Sannikova, Natalia, Gerak, Chloe A. N., Shidmoossavee, Fahimeh S., King, Dustin T., Shamsi Kazem Abadi, Saeideh, Lewis, Andrew R., Bennet, Andrew J.
Biochemistry 2018 v.57 no.24 pp. 3378-3386
Citrobacter freundii, alpha-galactosidase, catalytic activity, deuterium, glycosides, hydrides, hydrolysis, isotopes, manganese, metal ions, strontium
The glycoside hydrolase family 4 (GH4) α-galactosidase from Citrobacter freundii (MelA) catalyzes the hydrolysis of fluoro-substituted phenyl α-d-galactopyranosides by utilizing two cofactors, NAD⁺ and a metal cation, under reducing conditions. In order to refine the mechanistic understanding of this GH4 enzyme, leaving group effects were measured with various metal cations. The derived βₗg value on V/K for strontium activation is indistinguishable from zero (0.05 ± 0.12). Deuterium kinetic isotope effects (KIEs) were measured for the activated substrates 2-fluorophenyl and 4-fluorophenyl α-d-galactopyranosides in the presence of Sr²⁺, Y³⁺, and Mn²⁺, where the isotopic substitution was on the carbohydrate at C-2 and/or C-3. To determine the contributing factors to the virtual transition state (TS) on which the KIEs report, kinetic isotope effects on isotope effects were measured on these KIEs using doubly deuterated substrates. The measured ᴰV/K KIEs for MelA-catalyzed hydrolysis of 2-fluorophenyl α-d-galactopyranoside are closer to unity than the measured effects on 4-fluorophenyl α-d-galactopyranoside, irrespective of the site of isotopic substitution and of the metal cation activator. These observations are consistent with hydride transfer at C-3 to the on-board NAD⁺, deprotonation at C-2, and a non-chemical step contributing to the virtual TS for V/K.