The subsite specificity of rat nardilysin was investigated using fluorogenic substrates of the type 2-aminobenzoyl-GGX 1 X 2 RKX 3 GQ-ethylenediamine-2,4-dinitrophenyl, where P 2 , P 2 , and P 3 residues were varied. (The nomenclature of Schechter and Berger (Schechter, I., and Berger, A. (1967) Biochem. Biophys. Res. Commun. 27, 157-162) is used where cleavage of a peptide occurs between the P 1 and P 1 residues, and adjacent residues are designated P 2 , P 3 , P 2 , P 3 , etc.) There was little effect on K m among different residues at any of these positions. In contrast, residues at each position affected k cat , with P 2 residues having the greatest effect. The S 3 , S 2 , and S 2 subsites differed in their amino acid preference. Tryptophan and serine, which produced poor substrates at the P 2 position, were among the best P 2 residues. The specificity at P 3 was generally opposite that of P 2 . Residues at P 2 , and to a lesser extent at P 3 , influenced the cleavage site. At the P 2 position, His, Phe, Tyr, Asn, or Trp produced cleavage at the amino side of the first basic residue. In contrast, a P 2 Ile or Val produced cleavage between the dibasic pair. Other residues produced intermediate effects. The pH dependence for substrate binding showed that the enzyme prefers to bind a protonated histidine. A comparison of the effect of arginine or lysine at the P 1 or P 1 position showed that there is a tendency to cleave on the amino side of arginine and that this cleavage produces the highest k cat values. Nardilysin (N-arginine dibasic convertase, EC 3.4.24.61) is a 130-kDa metallopeptidase and a member of the relatively newly discovered pitrilysin family of metallopeptidases, also referred to as the inverzincins. An active site zinc binding motif, HXXEH, which is inverted relative to the more common HEXXH motif (1), characterizes this family of metallopeptidases. The geometry and mechanism of peptide cleavage at an inverted zinc-binding site has not been elucidated. Aside from nardilysin, three other members of the pitrilysin family have been identified: insulin-degrading enzyme (EC 3.4.24.56) (2, 3), protease III from E. coli (EC 3.4.24.55) (4), and a recently described human metallopeptidase (5).Nardilysin is unique in that it contains an acidic region, which, depending on the particular species, is composed of 43 (human) to 59 (mouse) glutamate and aspartate residues within a 76-amino acid stretch. It has been suggested that this acidic domain might play a role in the regulation of nardilysin activity by forming charge-charge complexes with other cellular components (6, 7).The initial characterization of the specificity of nardilysin led to the conclusion that the enzyme cleaves peptide substrates on the amino side of an arginine residue of paired basic residues (8 -10). It has been found that although the enzyme cleaves a number of peptides between paired dibasic residues of the type Arg-Arg (dynorphin A, BAM12 residues 1-8) and Arg-Lys (␣-neoendorphin), with somatostatin 28 as substrate cleavage occurs ...