Ethyl dithioesters of N-acylglycine and N-acylalanine are shown to bind tightly to the active site of papain in which the side chain of cysteine-25 is in the mercurated form. Although both classes of dithioester bind to the active site mercury via their thiono (C=S) sulfur atoms, the resulting adducts are quite different. Absorption and resonance Raman data, supported by comparison with model compounds and by 15N and 13C=S isotopic substitutions, show that the glycine and alanine dithioesters are converted to enethiolates and 4-methyloxazolin-5-thiones, respectively. The difference in product formation is explained by a mechanism in which stereospecific proton removal is brought about by the -COO− side chain of Asp-158, which is situated in the vicinity of the active site. For glycine dithioesters the Asp-158 catalyses the removal of a Cα proton whereas for alanine dithioesters the alanine's NH proton is removed.