Trypsin: a case study in the structural determinants of enzyme specificity

Abstract

Trypsin and chymotrypsin have similar tertiary structures, although very different substrate specificities. Trypsin hydrolyzes peptides at Lys/Arg residues while chymotrypsin recognizes large hydrophobic residues. Recent work has shown that trypsin is not converted into a protease with chymotrypsin-like activity when the S1 substrate binding site residues are replaced with their chymotrypsin counterparts. Chymotrypsin-like activity is reconstituted in the trypsin framework when two surface loops are substituted with the analogous loops of chymotrypsin in addition to the substitutions at the S1 site. Chymotrypsin-like activity is further improved when Tyr172, another residue located outside the S1 site, is replaced with Trp. These mutant enzymes catalyze the hydrolysis of enzyme-bound substrate at rates comparable to chymotrypsin, but are defective in substrate binding. X-ray crystal structures of the chymotrypsin-like mutants reveal that the loops are disordered and that the Tyr172 to Trp substitution stabilizes the loops. These observations demonstrate that substrate specificity is derived from a network of structural interactions which extends beyond the S1 site.