Structural basis of perturbed pK_a values of catalytic groups in enzyme active sites

In protein and RNA macromolecules, only a limited number of different side-chain chemical groups are available to function as catalysts. The myriad of enzyme-catalyzed reactions results from the ability of most of these groups to function either as nucleophilic, electrophilic, or general acid-base catalysts, and the key to their adapted chemical function lies in their states of protonation. Ionization is determined by the intrinsic pK_a of the group and the microenvironment created around the group by the protein or RNA structure, which perturbs its intrinsic pK_a to its functional or apparent pK_a. These pK_a shifts result from interactions of the catalytic group with other fully or partially charged groups as well as the polarity or dielectric of the medium that surrounds it. The electrostatic interactions between ionizable groups found on the surface of macromolecules are weak and cause only slight pK_a perturbations (<2 units). The sum of many of these weak electrostatic interactions helps contribute to the stability of native or folded macromolecules and their ligand complexes. However, the pK_a values of catalytic groups that are found in the active sites of numerous enzymes are significantly more perturbed (>2 units) and are the subject of this review. The magnitudes of these pK_a perturbations are analyzed with respect to the structural details of the active-site microenvironment and the energetics of the reactions that they catalyze.