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

Christian Rapp, Annika Borg and Bernd Nidetzky ()
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Christian Rapp: Graz University of Technology, NAWI Graz
Annika Borg: Graz University of Technology, NAWI Graz
Bernd Nidetzky: Graz University of Technology, NAWI Graz

Nature Communications, 2024, vol. 15, issue 1, 1-10

Abstract: 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 ( $${\Delta {{{{{\rm{H}}}}}}}^{{{\ddagger}} }$$ Δ H ‡ = 54 kJ mol−1), significant loss in entropy ( $$-T{\Delta {{{{{\rm{S}}}}}}}^{{{\ddagger}} }$$ − T Δ S ‡ = 20 kJ mol−1; 298 K) and negative activation heat capacity ( $${\Delta {{{{{\rm{C}}}}}}}_{{{{{{\rm{p}}}}}}}^{{{\ddagger}} }$$ Δ 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.

Date: 2024
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DOI: 10.1038/s41467-024-48281-6

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