All serine proteases follow the same mechanism. Their specificity is determined by the nature of the specificity pocket. In the trypsin specificity pocket, the basic residue of the substrate interacts with an Asp at the bottom of the pocket. Divergent Evolution of Enzymes - Substrate specificity of pancreatic serine proteases. The serine proteases all have the same substrate, a polypeptide chain.
Different enzymes cleave the chain adjacent to different amino acids.
Convergent Evolution of Enzymes - Chymotrypsin and Subtilisin. Subtilisins are a group of serine proteases produced by bacteria. Both chymotrypsins and subtilisins hydrolyze polypeptide chains adjacent to large hydrophobic amino acid side chains - they have the same specificity. Yet, the subtilisins and chymotrypsins have no amino acid sequence similarity and their tertiary structures are quite different. Chymotrypsin is composed of primarily b -sheets and the active site lies between two distinct domains.