Matriptase is a type II transmembrane serine protease comprising 855 amino acid residues. The extracellular region of matriptase comprises a noncatalytic stem domain (containing two tandem repeats of complement proteases C1r/C1s-urchin embryonic growth factor-bone morphogenetic protein (CUB) domain) and a catalytic serine protease domain. The stem domain of matriptase contains site(s) for facilitating the interaction of this protease with the endogenous inhibitor, hepatocyte growth factor activator inhibitor type-1 (HAI-1). The present study aimed to identify these site(s had no effect. HAI-1-58K precipitated with immobilized streptavidin resins to which a synthetic peptide Val 380 -Pro 392 with a biotinylated lysine residue at its C terminus was bound, suggesting direct interaction between CUB domain II and HAI-1. These results led to the identification of the matriptase CUB domain II, which facilitates the primary inhibitory interaction between this protease and HAI-1.Matriptase (also known as epithin, membrane-type serine protease 1, SNC19, suppression of tumorigenicity 14) is a transmembrane serine protease (1-7). This protease belongs to the type II transmembrane serine protease group, which is characterized by an N-terminal cytoplasmic domain, a signal anchor transmembrane domain, and an extracellular C-terminal serine protease catalytic domain (8,9). Matriptase is first synthesized as a zymogen comprising 855 amino acid residues in the human, mouse, and rat (7,10,11). Interaction between the zymogens appears to result in the generation of disulfidelinked two-chain molecules with an N-terminal Val 615 (activated matriptase molecules) (Fig. 1A) (10, 12-16). In addition, matriptase appears to function both as a plasma membraneassociated form and as a shed (soluble) form (1, 15, 17). The two-chain matriptase purified from human milk exhibits activity with trypsin-like specificity and is known to cleave and thus activate single-chain urokinase-type plasminogen activator (scuPA) 2 and pro-hepatocyte growth factor (pro-HGF) (18). Bacterially expressed variants of the recombinant (r-) catalytic domain of matriptase also cleaved to activate sc-uPA (19) and pro-HGF (20). Another r-matriptase catalytic domain cleaved to activate the precursor form of prostasin, a glycosylphosphatidylinositol-linked serine protease (3, 21). Together with the abundant expression in epithelial cells and in keratinocytes (7,22,23), these characteristics lead to the proposition that matriptase plays a key role in the maintenance of epithelial integrity and homeostasis. Studies in genetically manipulated mice indicate the importance of matriptase for epithelial and epidermal barrier function (24 -27).In general, members of the type II transmembrane serine protease group have an extracellular noncatalytic stem domain comprising various structural motifs (8, 9). For instance, the stem domain of matriptase comprises a sea-urchin sperm protein-enteropeptidase-agrin (SEA) domain, followed by two tandem repeats of complement proteases C1r/C1s-u...