The fibrillar collagen types I, II, and V/XI have recently been shown to have partially 3-hydroxylated proline (3Hyp) residues at sites other than the established primary Pro-986 site in the collagen triple helical domain. These sites showed tissue specificity in degree of hydroxylation and a pattern of D-periodic spacing. This suggested a contributory role in fibril supramolecular assembly. The sites in clade A fibrillar ␣1(II), ␣2(V), and ␣1(I) collagen chains share common features with known prolyl 3-hydroxylase 2 (P3H2) substrate sites in ␣1(IV) chains implying a role for this enzyme. We pursued this possibility using the Swarm rat chondrosarcoma cell line (RCS-LTC) found to express high levels of P3H2 mRNA. Mass spectrometry determined that all the additional candidate 3Hyp substrate sites in the pN type II collagen made by these cells were highly hydroxylated. In RNA interference experiments, P3H2 protein synthesis was suppressed coordinately with prolyl 3-hydroxylation at Pro-944, Pro-707, and the C-terminal GPP repeat of the pN␣1(II) chain, but Pro-986 remained fully hydroxylated. Furthermore, when P3H2 expression was turned off, as seen naturally in cultured SAOS-2 osteosarcoma cells, full 3Hyp occupancy at Pro-986 in ␣1(I) chains was unaffected, whereas 3-hydroxylation of residue Pro-944 in the ␣2(V) chain was largely lost, and 3-hydroxylation of Pro-707 in ␣2(V) and ␣2(I) chains were sharply reduced. The results imply that P3H2 has preferred substrate sequences among the classes of 3Hyp sites in clade A collagen chains.Collagen, the major structural protein of vertebrates has evolved a range of post-translational modifications that are essential for triple helix assembly and stability, intermolecular cross-linking, and strength of fibrils and tissue function. Enzymes from the family of 2-oxo-glutarate-dependent dioxygenases are responsible for most of these modifications. For example, prolyl 4-hydroxylase catalyzes proline 4-hydroxylation, a modification necessary for the secondary and tertiary structure of collagen (1, 2), and the lysyl hydroxylase isoenzymes catalyze lysine hydroxylation, a modification essential for the formation of intermolecular cross-links in collagen (2-4).Prolyl 3-hydroxlase 1 (P3H1), 2 another member of the 2-oxo-glutarate-dependent dioxygenase family, catalyzes the post-translational 3-hydroxylation of certain proline residues in fibril-forming collagens. This enzyme was only recently cloned from chicken tissues (5) after being partially purified Ͼ25 years ago (6). P3H1 was identified as the chick homologue of rat leprecan, a glycoprotein, which was first isolated from a rat parietal yolk sac tumor cell line (7). Within the past few years, novel mutations in the human P3H1 gene and genes encoding P3H1-associated proteins were shown to cause recessive forms of osteogenesis imperfecta (8 -11). By mass spectrometry, we and other investigators have shown that Pro-986 in the ␣1(I) collagen chain of bone and skin from such patients can be severely under-3-hydroxyated. The P3H1 enz...