N-Deacetylation and N-sulfation of N-acetylglucosamine of heparin and heparan sulfate are hypothesized to be mediated by different tissue-specific N-acetylglucosaminyl N-deacetylases/N-sulfotransferases, which in turn lead to the higher L-iduronic acid and sulfate content of heparin versus heparan sulfate. Furthermore, the putative heparin-specific N-acetylglucosaminyl Ndeacetylase/N-sulfotransferase has been reported to require auxiliary proteins for its N-acetylglucosaminyl Ndeacetylase activity in vivo based on its requirement of polycations in vitro. We have now found that cells derived from embryonic bovine trachea, a tissue that does not synthesize heparin, has a N-acetylglucosaminyl Ndeacetylase/N-sulfotransferase, which has 95% amino acid sequence identity to the above enzyme postulated to be involved in the biosynthesis of heparin. Both enzymes also have very similar affinity for their substrates. The trachea enzyme does not require additional effectors for its N-acetylglucosaminyl N-deacetylase activity in vitro even though its biochemical characteristics are virtually the same as the enzyme previously isolated from cells of a heparin-producing mastocytoma tumor. The trachea enzyme, which is encoded by an abundant 4.6-kilobase mRNA, like mastocytoma cells, has 70% amino acid sequence identity with the corresponding enzyme from rat liver postulated to participate in the biosynthesis of heparan sulfate. Heparan sulfate synthesized by trachea cells has a higher content of sulfated iduronic acid than from other tissues. Together, the above results strongly suggest that the above enzymes from mastocytoma, liver, and trachea, per se, are not solely responsible for the selective tissue-specific synthesis of heparin or heparan sulfate; more likely cellular factors, additional enzymes, and availability of substrates in the Golgi lumen also play important roles in the differential synthesis of the above proteoglycans.Heparan sulfate and heparin are proteoglycans with sulfated glycosaminoglycans of alternating glucosamine and uronic acid; heparin has a higher content of iduronic acid and sulfate than heparan sulfate. The latter plays biological roles in cell recognition (1), cell adhesion (2, 3), developmental regulation of neural tissues (4), and as receptor for endocytosis (5), basic fibroblast growth factor (6 -8), and viruses (9), whereas heparin is involved in blood clotting (10). Heparin and heparan sulfate also occur in different tissues, the latter being present in virtually all mammalian ones, whereas heparin is restricted to connective tissue mast cells (11). Nevertheless, they appear to share biosynthetic pathways, beginning with the polymerization of glucuronic acid and N-acetylglucosamine, followed by the N-deacetylation and N-sulfation of N-acetylglucosamine, subsequent epimerization of glucuronic acid to L-iduronic acid, 2-O-sulfation of this latter sugar and 6-O-sulfation of glucosamine (12). Heparin, in addition, undergoes 3-O-sulfation of this latter sugar.Up to now, proteins from rat liver (13,...