Cathepsin C, a lysosomal dipeptidyl aminopeptidase, is competitively and reversibly inhibited by guanidinium ions with a K-i approximate to 1.5 mM, Loss of activity is not the result of conformational change, subunit dissociation or altered mobility of the enzyme, but rather reflects a specific binding of guanidinium ions to the active site. The finding that cathepsin C is not inhibited by substrate has allowed the kinetic parameters in the presence of guanidinium ion to be determined, Guanidinium significantly decreases the K-m of substrate hydrolysis, without changing V-max. In a novel application of the transferase reaction, the K-m of the nucleophile substrate has been determined (11 mM) and found not to be affected by guanidinium, indicating its inhibition of substrate binding to the S, but not the S', site, Inhibition is suggested to be the result of shielding a negative charge on the enzyme important for interaction with the substrate. (C) 1999 Academic Press.