The human lysyl oxidase-like 3 (LOXL3) encodes a member of the emerging family of lysyl oxidase (LOX) that functions as a copper-dependent amine oxidase. The LOXL3 protein contains four scavenger receptor cysteine-rich domains in the N terminus in addition to the C-terminal characteristic domains of the LOX family, such as a copper binding domain, a cytokine receptor-like domain and residues for the lysyl-tyrosyl quinone cofactor. Using BLASTN searches, we identified a LOXL3 variant LOXL3-sv1 that lacked the sequences corresponding to exons 1, 2, 3, and 5 of LOXL3. LOXL3-sv1 showed an exon-intron structure distinct from LOXL3, additionally containing an 80-bp sequence corresponding to intron 3 of LOXL3 in the 5 -UTR and a 561-bp sequence corresponding to the 3 -flanking genomic region of exon 14 in the 3 -UTR. LOXL3-sv1 was predicted to encode a polypeptide of 392 amino acids that contains the C-terminal domains required for amine oxidase activity but lacks the N-terminal SRCR domains 1, 2, and 3. The recombinant LOXL3-sv1 protein showed a -aminopropionitrile-inhibitable amine oxidase activity toward elastin and collagen with substrate specificity. In RT-PCR assays with various human tissues, LOXL3-sv1 and LOXL3 showed distinct expression patterns. Further, luciferase reporter assays revealed a strong promoter element in intron 3 that probably functions as a regulatory region for the expression of LOXL3-sv1. These findings strongly indicate that LOXL3 encodes two variants, LOXL3 and LOXL3-sv1, both of which function as amine oxidases with distinct tissue and substrate specificities from one another.Lysyl oxidase (LOX), 2 a copper-dependent amine oxidase, is responsible for the development of lysine-derived cross-links in extracellular matrix proteins, such as collagen and elastin (1). LOX oxidizes the epsilon amino groups of peptidyl lysines to reactive aldehydes. The resulting aldehyde groups then undergo spontaneous condensation with unreacted epsilon amino groups or neighboring aldehyde groups, converting collagen or elastin monomers into insoluble fibers (2, 3). The LOX-mediated cross-linkage of collagen or elastin monomers is an essential step for the biogenesis of fibrillar extracellular matrix in most tissues.Recent molecular cloning has revealed the existence of a human LOX family consisting of the five paralogues LOX, LOXL, LOXL2, LOXL3, and LOXL4 (4 -8). Each LOX paralogue contains a copper-binding domain, residues for lysyl-tyrosyl quinone (LTQ) and a cytokine receptor-like (CRL) domain in the carboxyl (C) termini. The amino (N)-terminal regions of the LOX family members, in contrast, show little sequence homology except that LOXL2, LOXL3, and LOXL4 contain four repeated copies of scavenger receptor cysteinerich (SRCR) domains in their N termini. The SRCR domains, known to mediate the protein-protein interactions for cell adhesion and cell signaling, are found either on the cell surface proteins or secreted proteins (9, 10). The presence of SRCR domains within LOXL2, LOXL3, and LOXL4 indicates that t...