Glucuronyl C5-epimerases catalyze the conversion of D-glucuronic acid (GlcUA) to L-iduronic acid (IdceA) units during the biosynthesis of glycosaminoglycans. An epimerase implicated in the generation of heparin/heparan sulfate was previously purified to homogeneity from bovine liver (Campbell, P., Hannesson, H. H., Sandback, D., Roden, L., Lindahl, U., and Li, J.-p, (1994) J. Biol. Chem. 269, 2695-26958). The present report describes the molecular cloning and functional expression of the lung enzyme, The cloned enzyme contains 444 amino acid residues and has a molecular mass of 49,905 Da, N-terminal sequence analysis of the isolated liver enzyme showed this species to be a truncated form lacking a 73-residue N-terminal domain of the deduced amino acid sequence. The coding cDNA insert was cloned into a baculovirus expression vector and expressed in Sf9 insect cells, Cells infected with recombinant epimerase showed a 20-30-fold increase in enzyme activity, measured as release of (H2O)-H-3 from a polysaccharide substrate containing C5-H-3-labeled hexuronic acid units. Furthermore, incubation of the expressed protein with the appropriate (GlcUA-GlcNSO(3))(n) substrate resulted in conversion of similar to 20% of the GlcUA units into IdceA residues, Northern analysis implicated two epimerase transcripts in both bovine lung and liver tissues, a dominant similar to 9-kilobase (kb) mRNA and a minor similar to 5-kb species, Mouse mastocytoma cells showed only the similar to 5-kb transcript. A comparison of the cloned epimerase with the enzymes catalyzing an analogous reaction in alginate biosynthesis revealed no apparent amino acid sequence similarity.