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Type IX collagen is a recently characterized product of chondrocytes. The molecules of this collagen are heterotrimers of three genetically distinct polypeptide chains. One of the three chains contains chondroitin and/or dermatan sulfate glycosaminoglycan chains, giving the molecule a proteoglycan character. In fact, Type IX collagen has been identified with the proteoglycan Lt (PG-Lt), first isolated by Noro, A., Kimata, K., Oike, Y., Shinomura, T., Maeda, N., Yano, S., Takahashi, N., and Suzuki, S. (1983) J. Biol. Chem. 258, 9323-9331 from chick embryonic tibia and femur. Based on amino acid sequences predicted from the nucleotide sequences of cDNA and genomic clones specific for two of the chains of Type IX collagen, we have synthesized oligopeptides representing portions of the two chains. In addition, an oligopeptide has been made based on a partial amino acid sequence of the third chain. Antibodies against the synthetic peptides have been generated in rabbits, and the polyclonal sera have allowed identification of the three genetically distinct polypeptide subunits of Type IX collagen. In addition, labeling with [35S]sulfate and treatment with chondroitinase ABC demonstrates that glycosaminoglycan chains are present on the subunit that has been given the designation alpha 2(IX).

Type IX collagen in cartilage consists of molecules composed of three genetically distinct polypeptide subunits. One of the subunits, alpha 2(IX), contains a covalently attached glycosaminoglycan side chain whereas a second subunit, alpha 1(IX), contains a large noncollagenous, amino-terminal domain called NC4. In this report, we describe for the first time the complete primary structure of this noncollagenous domain, based on cloning and sequencing of cDNA and genomic DNA as well as amino acid sequencing of tryptic peptides. Analysis of genomic clones has also allowed determination of the exon structure of NC4. Our results demonstrate that the noncollagenous, amino-terminal domain of alpha 1(IX) chains contains 266 amino acid residues (including the signal peptide) with 5 cysteinyl residues forming two disulfide bridges. The domain is basic with an estimated pI of 9.7, thus supporting the idea that it may participate in ionic interactions with polyanionic glycosaminoglycans in cartilage. Both the sequence and exon structure of the NC4 domain is unique among collagens and there is no obvious homology with the noncollagenous domains of other types of collagen, including the propeptides of fibrillar collagens.