The 300-kDa cation-independent mannose 6-phosphate receptor (CI-MPR), which contains multiple mannose 6-phosphate (Man-6-P) binding sites that map to domains 3, 5, and 9 within its 15-domain extracytoplasmic region, functions as an efficient carrier of Man-6-P-containing lysosomal enzymes. To determine the types of phosphorylated N-glycans recognized by each of the three carbohydrate binding sites of the CI-MPR, a phosphorylated glycan microarray was probed with truncated forms of the CI-MPR. Surface plasmon resonance analyses using lysosomal enzymes with defined N-glycans were performed to evaluate whether multiple domains are needed to form a stable, high affinity carbohydrate binding pocket. Like domain 3, adjacent domains increase the affinity of domain 5 for phosphomannosyl residues, with domain 5 exhibiting ϳ60-fold higher affinity for lysosomal enzymes containing the phosphodiester Man-P-GlcNAc when in the context of a construct encoding domains 5-9. In contrast, domain 9 does not require additional domains for high affinity binding. The three sites differ in their glycan specificity, with only domain 5 being capable of recognizing Man-P-GlcNAc. In addition, domain 9, unlike domains 1-3, interacts with Man 8 GlcNAc 2 and Man 9 GlcNAc 2 oligosaccharides containing a single phosphomonoester. Together, these data indicate that the assembly of three unique carbohydrate binding sites allows the CI-MPR to interact with the structurally diverse phosphorylated N-glycans it encounters on newly synthesized lysosomal enzymes.The 300-kDa cation-independent mannose 6-phosphate receptor (CI-MPR), 4 along with the smaller 46-kDa homodimeric cation-dependent mannose 6-phosphate receptor (CD-MPR), play an essential role in the degradative metabolism of cells by delivering ϳ60 different mannose 6-phosphate (Man-6-P)-tagged lysosomal enzymes from the secretory pathway to the endosomal/lysosomal system. Newly synthesized lysosomal enzymes are modified with phosphomannosyl residues on their N-glycans as they traverse the Golgi (1-3). In early Golgi compartments, UDP-N-acetylglucosamine:lysosomal enzyme N-acetylglucosamine-1-phosphotransferase (GlcNAc phosphotransferase; IUBMB accession number EC 2.7.8.17), adds N-acetylglucosamine (GlcNAc)-1-phosphate to the C-6 hydroxyl group of mannose residues to form a phosphodiester, Man-P-GlcNAc ( Fig. 1) (4 -7). The second enzyme, N-acetylglucosamine-1-phosphodiester ␣-N-acetylglucosaminidase (uncovering enzyme) (IUBMB accession number EC 3.1.4.45), removes the GlcNAc moiety in the trans Golgi network to generate a phosphomonoester ( Fig. 1) (8 -12). This recognition system is critical for normal development because a genetic defect in GlcNAc phosphotransferase causes the lysosomal storage disorders mucolipidosis II and III, with the more severe of these disorders, mucolipidosis II, resulting in death often within the first decade of life (13). The CI-MPR has been shown to be more efficient in targeting lysosomal enzymes to the lysosome than the CD-MPR, both in vitro (14, 15) and in vi...