Combined in vitro and in silico analyses of missense mutations in GNPTAB provide new insights into the molecular bases of mucolipidosis II and III alpha/beta

Mucolipidosis (ML) II and III alpha/beta are inherited lysosomal storage disorders caused by mutations in GNPTAB encoding the α/β‐precursor of GlcNAc‐1‐phosphotransferase. This enzyme catalyzes the initial step in the modification of more than 70 lysosomal enzymes with mannose 6‐phosphate residues to ensure their intracellular targeting to lysosomes. The so‐called stealth domains in the α‐ and β‐subunit of GlcNAc‐1‐phosphotransferase were thought to be involved in substrate recognition and/or catalysis. Here, we performed in silico alignment analysis of stealth domain‐containing phosphotransferases and showed that the amino acid residues Glu³⁸⁹, Asp⁴⁰⁸, His⁹⁵⁶, and Arg⁹⁸⁶ are highly conserved between different phosphotransferases. Interestingly, mutations in these residues were identified in patients with MLII and MLIII alpha/beta. To further support the in silico findings, we also provide experimental data demonstrating that these four amino acid residues are strictly required for GlcNAc‐1‐phosphotransferase activity and thus may be directly involved in the enzymatic catalysis.