Detection of large pK_a perturbations of an inhibitor and a catalytic group at an enzyme active site, a mechanistic basis for catalytic power of many enzymes

Δ⁵-3-Ketosteroid isomerase catalyzes cleavage and formation of a C-H bond at a diffusion-controlled limit. By determining the crystal structures of the enzyme in complex with each of three different inhibitors and by nuclear magnetic resonance (NMR) spectroscopic investigation, we evidenced the ionization of a hydroxyl group (pK_a ∼16.5) of an inhibitor, which forms a low barrier hydrogen bond (LBHB) with a catalytic residue Tyr¹⁴ (pK_a ∼11.5), and the protonation of the catalytic residue Asp³⁸ with pK_a of ∼4.5 at pH 6.7 in the interaction with a carboxylate group of an inhibitor. The perturbation of the pK_a values in both cases arises from the formation of favorable interactions between inhibitors and catalytic residues. The results indicate that the pK_a difference between catalytic residue and substrate can be significantly reduced in the active site environment as a result of the formation of energetically favorable interactions during the course of enzyme reactions. The reduction in the pK_a difference should facilitate the abstraction of a proton and thereby eliminate a large fraction of activation energy in general acid/base enzyme reactions. The pK_a perturbation provides a mechanistic ground for the fast reactivity of many enzymes and for the understanding of how some enzymes are able to extract a proton from a C-H group with a pK_a value as high as ∼30.