Catalytic triad

A catalytic triad commonly refers to the three amino acid residues found inside the active site of certain protease enzymes: serine (S), aspartate (D) and histidine (H). They work together to break peptide bonds on polypeptides. More generally, catalytic triad can refer to any set of three residues that function together and are directly involved in catalysis. Because enzymes fold into complex three-dimensional shapes, the residues of a catalytic triad can be far from each other in the primary structure however are brought close together in the tertiary structure.

Example
An example of a catalytic triad is present in chymotrypsin, where the triad (on the enzyme) consists of S195 (that is the serine found at residue 195 in the protein sequence), D102 and H57. Essentially, S195 binds to the substrate polypeptide to the side of a phenylalanine, tryptophan or tyrosine residue closer to the C-terminus, holding it in place. D102 and H57 then hydrolyze the bond. This takes place in several steps.


 * 1) Upon binding of the target protein, the carboxylic group (-COOH) on D102 forms a low-barrier hydrogen bond with H57, increasing the pKa of its imidazole nitrogen from 7 to about 12. This allows H57 to act as a powerful general base, and deprotonate S195.
 * 2) The deprotonated S195 serves as a nucleophile, attacking the carbonyl carbon on the C-terminal side of the residue and forcing the carbonyl oxygen to accept an electron, and transforming the sp2 carbon into a tetrahedral intermediate. This intermediate is stabilized by an oxanion hole, which also involves S195.
 * 3) Collapse of this intermediate back to a carbonyl causes H57 to donate its proton to the nitrogen attached to the alpha carbon. The nitrogen and the attached peptide fragment (c-terminal to the F W or Y residue) leave by diffusion.
 * 4) A water molecule then donates a proton to H57 and the remaining OH- attacks the carbonyl carbon, forming another tetrahedral intermediate. The OH is a worse leaving group than the C-terminal fragment, so when the tetrahedral intermediate collapses again, S195 leaves and regains a proton from H57.
 * 5) The cleaved peptide, now with a carboxyl end, leaves by diffusion.