A cDNA encoding a novel matrix metalloproteinase (MMP) was isolated from a porcine enamel organ-specific cDNA library. Multiple tissue northern blot analysis revealed the presence of two mRNA transcripts which were expressed only in the enamel organ. The transcripts were 1968 bp or 3420 bp in length and resulted from the utilization of alternative polyadenylation sites. The open reading frame of the cloned mRNA encodes a protein composed of 483 amino acids. The MMP has a predicted molecular mass of 54.1 kDa, which is similar to that of the stromelysins or collagenases, although it is not a member of either of these two classes of MMPs. A motif analysis revealed that the cloned MMP does not contain a consensus hemopexin-like domain because it lacks a critical tryptophan and proline residue at the appropriate positions. Since the cloned MMP is a new member of the MMP gene family and its expression appears limited to the enamel organ, we have named it enamelysin.