Divergence of substrate specificity within the context of a common structural framework represents an important mechanism by which new enzyme activity naturally evolves. We present enzymological and x-ray structural data for hamster chymase-2 (HAM2) that provides a detailed explanation for the unusual hydrolytic specificity of this rodent ␣-chymase. In enzymatic characterization, hamster chymase-1 (HAM1) showed typical chymase proteolytic activity. In contrast, HAM2 exhibited atypical substrate specificity, cleaving on the carboxyl side of the P1 substrate residues Ala and Val, characteristic of elastolytic rather than chymotryptic specificity. The 2.5-Å resolution crystal structure of HAM2 complexed to the peptidyl inhibitor MeOSuc-Ala-Ala-Pro-Ala-chloromethylketone revealed a narrow and shallow S1 substrate binding pocket that accommodated only a small hydrophobic residue (e.g. Ala or Val form an easily identifiable triplet in all known rodent ␣-chymases that can be used to predict elastolytic specificity for novel chymase-like sequences. Phylogenetic comparison defines guinea pig and rabbit chymases as the closest orthologs to rodent ␣-chymases.Chymases (EC 3.4.21.39), serine proteases with a chymotrypsin-fold, are stored within the secretory granules of mast cells along with histamine, tryptases, and other inflammation mediators. When released during mast cell degranulation in various tissues, chymases participate in a variety of biological functions including regulation of vasoactive peptide processing, modulation of inflammatory response, stimulation of submucosal gland secretion, and degradation of extracellular matrix (1). Human chymase has been linked to various pathologic conditions such as allergic inflammatory reactions that can contribute to asthma (2), Crohn disease (3), inflammatory kidney disease (4), and cardiovascular disorders (5, 6).Based on the catalytic triad consisting of His, Asp, and Ser (in that order in the sequence), chymases belong to the S1A family of serine proteases that include, for example, trypsin, chymotrypsin, elastase, and cathepsin G (7, 8). Mammalian chymases divide into two phylogenetic groups, termed ␣-and -chymases (9 -11). The genomes of primates, dogs, ruminants, and rodents apparently contain only one functional ␣-chymase, whereas rodents typically have several -chymases. Until recently, all chymases were thought to possess chymotryptictype substrate specificity, preferring Tyr and Phe (as well as Trp and Leu, to a lesser extent) at the P1 substrate position (Schechter and Berger nomenclature (12)). However, two recent studies have clearly established elastolytic specificity (i.e. preference for small aliphatic residues Ala, Val, and Ile at the P1 position) for mouse chymase-5 (mouse mast cell protease-5; mMCP5) 4 and rat chymase-5 (rMCP5) (13,14). Neither enzyme hydrolyzed a typical chymase substrate with Phe at P1. Site-directed mutagenesis and computer modeling studies suggested Val 216 as a major contributor to this unusual substrate specificity (14).Hamster ch...