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The UDP-Glc NAc:lysosomal enzyme, N-acetylglucosamine-1-phosphotransferase (Glc NAc-1- PT), is an α2β2γ2 hexamer that mediates the initial step in the formation of the mannose 6-phosphate targeting signal on newly synthesized lysosomal acid hydrolases. The GNPTAB gene encodes the 1256 amino acid long α/β precursor which is normally cleaved at K928 in the early Golgi by Site-1 protease (S1P). Here, we show that removal of the so-called 'spacer-1′ domain (residues 86-322) results in cleavage almost exclusively at a second S1P consensus sequence located upstream of K928. In addition, Glc NAc-1- PT lacking spacer-1 exhibits enhanced phosphorylation of several non-lysosomal glycoproteins, while the phosphorylation of lysosomal acid hydrolases is not altered. In view of these effects on the maturation and function of Glc NAc-1- PT, we suggest renaming `spacer-1′ the `regulatory-1′ domain. [ABSTRACT FROM AUTHOR]