Meprin A and B are highly regulated, secreted, and cell-surface metalloendopeptidases that are abundantly expressed in the kidney and intestine. Meprin oligomers consist of evolutionarily related ␣ and/or  subunits. The work herein was carried out to identify bioactive peptides and proteins that are susceptible to hydrolysis by mouse meprins and kinetically characterize the hydrolysis. Gastrin-releasing peptide fragment 14 -27 and gastrin 17, regulatory molecules of the gastrointestinal tract, were found to be the best peptide substrates for meprin A and B, respectively. Peptide libraries and a variety of naturally occurring peptides revealed that the meprin  subunit has a clear preference for acidic amino acids in the P1 and P1 sites of substrates. The meprin ␣ subunit selected for small (e.g. serine, alanine) or hydrophobic (e.g. phenylalanine) residues in the P1 and P1 sites, and proline was the most preferred amino acid at the P2 position. Thus, although the meprin ␣ and  subunits share 55% amino acid identity within the protease domain and are normally localized at the same tissue cell surfaces, they have very different substrate and peptide bond specificities indicating different functions. Homology models of the mouse meprin ␣ and  protease domains, based on the astacin crystal structure, revealed active site differences that can account for the marked differences in substrate specificity of the two subunits.Meprin A and B are zinc metalloendopeptidases composed of evolutionarily related ␣ and/or  subunits. They are members of the astacin family and are highly expressed in brush border membranes of the intestine and renal proximal tubules (1, 2). Meprins are particularly abundant in mouse juxtamedullary nephrons and constitute ϳ5% of total protein in renal brush border membranes (3). The meprin ␣ and  subunits are expressed early in embryonic development of mouse kidney and intestine, by day 11, and have different patterns of expression in the suckling phase and after weaning (4). Homologous enzymes are found in rat and human kidney and intestine (1,5,6). Meprins are also expressed in leukocytes of intestinal lamina propria and in cancer cells and are consequently implicated in inflammation and cancer growth and metastasis (7,8).Mouse kidney meprin A (EC 3.4.24.18) is a homooligomer of ␣ subunits, or a heterooligomer of ␣ and  subunits (2, 9). Mouse kidney meprin B (EC 3.4.24.63) is a homooligomer of  subunits (10). The multidomain ␣ and  meprin subunits are highly glycosylated and form disulfide-linked dimers and higher order oligomers by noncovalent interactions (11,12). Meprins containing at least one  subunit remain membranebound by virtue of a transmembrane domain located near the carboxyl terminus of  subunits (1). Mature meprin ␣ homooligomers contain no transmembrane domain and are found in mouse urine (13). The expression of the meprin ␣ subunits in mice is strain-dependent (1). Random-bred mice (such as ICR) and many inbred strains of mice (e.g. C57BL/6) express both meprin ␣ and  in...