Matrix vesicles (MV) initiate de novo mineralization in a variety of vertebrate-calcifying tissues. In recent studies, a quantitatively major group of MV proteins, the acidic phospholipid-dependent Ca2(+)-binding proteins (APD-CaBP) were found to be immunologically related to the annexin family of proteins that possess phospholipase A2 inhibitory activity. This finding helped explain the enrichment of phosphatidylserine as well as the presence of large amounts of complexed Ca2+ noted previously in these structures. To characterize further these annexin-like proteins, preparations of both collagenase-released MV and MV-enriched microsomes were subjected to a differential fractionation process that led to the isolation and purification to homogeneity of two of the MV APD-CaBP, a 33-kDa protein and a 36-kDa calpactin II-like protein. Polyclonal antibodies raised to each pure protein were found not to cross-react with the other, thus indicating two distinctive proteins. Measurement of the phosphatidylserine-dependent Ca2(+)-binding properties of the proteins revealed apparent Kd values of 2.5 x 10(-7) and 5.0 x 10(-7) M for the 36- and 33-kDa proteins, respectively. Such high affinities indicate that both proteins would be normally bound to the membrane of MV. Immunological studies revealed the presence of both APD-CaBP in cultured growth plate chondrocytes but not in vesicles released into the culture medium. The finding of the 33-kDa but not the 36-kDa protein in vesicles released from the calcifying matrix of the chondrocyte cultures by collagenase digestion may indicate a role for this protein in MV mineralization.