G(M1)-gangliosidosis and Morquio B disease are distinct in clinical and biochemical features, but both disorders are caused by genetic defects of the same enzyme, acid beta-galactosidase (beta-Gal). We analyzed the kinetic properties of mutant beta-Gals from patients with G(M1)-gangliosidosis and Morquio B disease to examine the clinical and biochemical differences between both disorders. Five skin fibroblast lines from patients with G(M1)-gangliosidosis (2 cases; R201C/R201C and I51T/I51T), Morquio B disease (2 cases; W273L/W273L and Y83H/R482C), and galactosialidosis (1 case; Y395C/S90L) were used as enzyme sources. Residual enzyme activity in the cells was subjected to kinetic analysis. Substrate analogs including Galbeta1-3GalNAc, as an analog for G(M1)-ganglioside, and Galbeta1-4GlcNAc, as an analog for keratan sulfate, were used to determine IC(50) and K(i) for beta-Gals with an artificial substrate (4-methylumbelliferyl beta-D-galactopyranoside). Enzymatic assay method was established to examine the hydrolytic activity with the mutant beta-Gal for the substrate analogs. The mutant beta-Gal activities were inhibited by Galbeta1-3GalNAc and Galbeta1-4GlcNAc in a concentration-dependent manner. Remarkable increase in IC(50) ratio and K(i) ratio (Galbeta1-4GlcNAc/Galbeta1-3GalNAc) was observed in Morquio B disease. Relative hydrolytic activity (Galbeta1-4GlcNAc/Galbeta1-3GalNAc) was markedly decreased in Morquio B disease as compared with other subjects; controls (means+/-SD, n=4), 1.00+/-0.02; galactosialidosis, 1.03; G(M1)-gangliosidosis, 1.15 and 1.00; and Morquio B disease, 0.27 and 0.32. The mutant beta-Gals from the patients with Morquio B disease exhibited lower affinity and lower hydrolytic activity toward Galbeta1-4GlcNAc rather than Galbeta1-3GalNAc. These findings suggest that imbalanced substrate specificity of the mutant beta-Gals induces predominant accumulation of keratan sulfate and a rationale for performing differential diagnostic analysis for both disorders.