The hydrolytic enzymes of lysosomes function best at pH:
Lysosomal acid hydrolases number about sixty different enzymes covering proteolysis, glycoside cleavage, lipid hydrolysis, nuclease activity and sulfatase action, each evolutionarily tuned for acidic environments to maximize substrate turnover and simultaneously protect cell from uncontrolled proteolysis if leakage occurs. Most display pronounced pH optima between 4.5 and 5.0, precisely matching steady-state lumen acidity maintained by vacuolar H+ ATPase delivering protons and chloride counter-transport via ClC-7 Cl-/H+ antiporter that prevents excessive voltage buildup. At this acidic pH catalytic aspartate residues in cathepsin D, histidine in cathepsin B and cysteine thiol in cathepsin L are correctly protonated for nucleophilic attack, substrate proteins are partially denatured exposing scissile bonds, and phosphodiester linkages become more labile. Mannose-6-phosphate receptors dissociate from newly delivered enzymes specifically at acidic pH after trafficking from trans-Golgi network, enabling enzyme retention. In contrast cytosolic pH 7.2 renders these enzymes largely inactive due to deprotonation, conformational closure and inhibitory cystatins. Experimental assays measuring cathepsin B, acid phosphatase, beta-hexosaminidase activity show sharp bell-shaped curves dropping above pH 6. Elevation of lysosomal pH by weak bases chloroquine, ammonium chloride or specific inhibitor bafilomycin A1 abolishes degradation, autophagic flux and cholesterol egress from NPC1 pathway, confirming dependence on low pH for function.
Ref: Alberts et al., Molecular Biology of the Cell, 6th ed., Chapter 13: Lysosomal Acid Hydrolases – pH Optimum 4.5.