User:Ann Taylor/Sandbox Trypsin

One of the ways we know about the mechanism of enzymes is through the use of xray crystallography structures of trapped intermediates or inhibitors bound to enzymes. In a paper by Radisky and Koshland^[1], an acyl intermediate of trypsin (PDB code 2AGG was characterized.

Serine proteases use a covalent mechanism to catalyze the hydrolysis of a peptide bond. A covalent bond is formed between Ser195 and a substrate peptide. The distance between one of the Ser O configurations and the alpha carbon of the substrate lysine is the distance of a C-O bond, indicating that the covalent intermediate is indeed formed. There is a water situated in the active site, primed to cleave the acyl intermediate by the same histidine that participates in the catalytic triad.

Specificity of the proteases is determined by a binding pocket. Trypsin is specific for large, basic amino acids; its binding pocket contains an aspartic acid residue at the base of the pocket.