Man9-mannosidase, one of three different alpha 1,2-exo-mannosidases known to be involved in N-linked oligosaccharide processing, has been cloned in lambda gt10, using a mixed-primed pig liver cDNA library. Three clones were isolated which allowed the reconstruction of a 2731-bp full-length cDNA. The cDNA construct contained a single open reading frame of 1977 bp, encoding a 659-residue polypeptide with a molecular mass of approximately 73 kDa. The Man9-mannosidase specificity of the cDNA construct was verified by the observation that all peptide sequences derived from a previously purified, catalytically active 49-kDa fragment were found within the coding region. The N-terminus of the 49-kDa fragment aligns with amino acid 175 of the translated cDNA, indicating that the catalytic activity is associated with the C-terminus. Transfection of COS 1 cells with the Man9-mannosidase cDNA gave rise to a > 30-fold over-expression of a 73-kDa protein whose catalytic properties, including substrate specificity, susceptibility towards alpha-mannosidase inhibitors and metal ion requirements, were similar to those of the 49-kDa enzyme fragment. Thus deletion of 174 N-terminal amino acids in the 73-kDa protein appears to have only marginal influence on the catalytic properties. Structural and hydrophobicity analysis of the coding region, as well as the results from tryptic degradation studies, point to pig liver Man9-mannosidase being a non-glycosylated type-II transmembrane protein. This protein contains a 48-residue cytosolic tail followed by a 22-residue membrane anchor (which probably functions as internal and non-cleavable signal sequence), a lumenal approximately 100-residue-stem region and a large 49-kDa C-terminal catalytic domain. As shown by immuno-fluorescence microscopy, the pig liver enzyme expressed in COS 1 cells, is resident in the endoplasmic reticulum, in contrast to COS 1 Man9-mannosidase from human kidney which is Golgi-located [Bieberich, E. & Bause, E. (1995) Eur. J. Biochem. 233, 644-649]. Localization of the porcine enzyme in the endoplasmic reticulum is consistent with immuno-electron-microscopic studies using pig hepatocytes. The different intracellular distribution of pig liver and human kidney Man9-mannosidase is, therefore, enzyme-specific rather than a COS-1-cell-typical phenomenon. Since we observe approximately 81% sequence similarity between the two alpha-mannosidases, we deduce that the localization in either endoplasmic reticulum or Golgi is likely to be sequence-dependent.