Structural Basis of Lysosomal Phospholipase A2 Inhibition by Zn2

Lysosomal Phospholipase A₂ (LPLA₂/PLA2G15) is a key Enzyme involved in lipid homeostasis and is characterized by both Phospholipase A2 and transacylase activity and by an acidic pH optimum. Divalent cations such as CA²⁺ and Mg²⁺ have previously been shown to have little effect on the activity of LPLA₂, but the discovery of a novel crystal form of LPLA₂ with Zn²⁺ bound in the active site suggested a role for this divalent cation in regulating Enzyme activity. In this complex, the cation directly coordinates the serine and histidine of the α/β-hydrolase triad and stabilizes a closed conformation. This closed conformation is characterized by an inward shift of the lid loop, which extends over the active site and effectively blocks access to one of its lipid acyl chain binding tracks. Therefore, we hypothesized that Zn²⁺ would inhibit LPLA₂ activity at a neutral but not acidic pH because histidine would be positively charged at lower pH. Indeed, Zn²⁺ was found to inhibit the esterase activity of LPLA₂ in a noncompetitive manner exclusively at a neutral pH (between 6.5 and 8.0). Because lysosomes are reservoirs of Zn²⁺ in cells, the pH optimum of LPLA₂ might allow it to catalyze acyl transfer unimpeded within the organelle. We conjecture that Zn²⁺ inhibition of LPLA₂ at higher pH maintains a lower activity of the esterase in environments where its activity is not typically required.