Prolyl endopeptidase catalysis. A physical rather than a chemical step is rate-limiting.

Prolyl endopeptidase represents a new family of serine proteases, and it has a mechanistic feature distinct from that of the enzymes of the extensively studied chymotrypsin and subtilisin families. The rate-determining step in the catalysis of serine proteases is a general base/acid-catalysed chemical step. For prolyl endopeptidase, however, the chemical step is not rate-limiting, as demonstrated by using substrates with different leaving groups. It is known that the acylation of chymotrypsin and subtilisin proceeds faster by several orders of magnitude with the activated nitrophenyl ester than with the corresponding amide substrates. In contrast, for the acylation of prolyl endopeptidase similar rate constants were obtained with nitrophenyl ester and several amide substrates. This result, combined with kinetic isotope studies [Polgár (1991) Eur. J. Biochem. 197, 441-447], offers strong evidence that a physical step, presumably a conformational change associated with substrate binding, is the rate-determining step in the prolyl endopeptidase catalysis.