Enzymes catalyze reactions under mild conditions that might otherwise require extreme conditions such as high temperature or strong acid or base. To achieve this, enzymes often impart exceptional chemical properties to amino acid side chains that, in the absence of the protein environment, would be far less reactive. For instance, amino acid side chains that would be weak Brønsted acids or bases in a small peptide can, in the enzymatic environment, become a strong base that can deprotonate a C-H bond or become a strong acid that can protonate the hydroxyl group of an alcohol. The primary amine side chain of a lysine residue, that would normally be protonated at neutral pH, can be deprotonated to become a nucleophile. Here we report on a set of 20 enzymes, representing all six major EC classes and a variety of different folds, for which experimental studies of the mechanistic roles of the catalytic residues have been reported in the literature. It is shown that the catalytic aspartate and glutamate residues are strongly coupled to at least one other aspartate or glutamate residue and often to multiple other carboxylate residues with intrinsic pKa differences less than 1 pH unit. Sometimes these catalytic acidic residues are also coupled to a histidine residue, such that the intrinsic pKa of the acidic residue is higher than that of the histidine. All catalytic lysine residues studied here are strongly coupled to tyrosine or cysteine residues, wherein the intrinsic pKa of the anion-forming residue is higher than that of the lysine. Some catalytic lysines are also coupled to other lysines with intrinsic pKa differences within 1 pH unit. Some general principles about the design of enzyme active sites are presented.

What gives amino acids their catalytic superpowers in the active sites of enzymes?

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