Interplay of structural preorganization and conformational sampling in UDP-glucuronic acid 4-epimerase catalysis

Abstract

Understanding enzyme catalysis as connected to protein motions is a major challenge. Here, based on temperature kinetic studies combined with isotope effect measurements, we obtain energetic description of C-H activation in NAD-dependent UDP-glucuronic acid C4 epimerase. Approach from the ensemble-averaged ground state (GS) to the transition state-like reactive conformation (TSRC) involves, alongside uptake of heat ( ${\Delta H}^{‡}$ = 54 kJ mol^-1), significant loss in entropy ( $-T{\Delta S}^{‡}$ = 20 kJ mol^-1; 298 K) and negative activation heat capacity ( ${\Delta C}_p^{‡}$ = -0.64 kJ mol^-1 K^-1). Thermodynamic changes suggest the requirement for restricting configurational freedom at the GS to populate the TSRC. Enzyme variants affecting the electrostatic GS preorganization reveal active-site interactions important for precise TSRC sampling and H-transfer. Collectively, our study captures thermodynamic effects associated with TSRC sampling and establishes rigid positioning for C-H activation in an enzyme active site that requires conformational flexibility in fulfillment of its natural epimerase function.