Lipid-organized tetramerization of PLPP1 defines the molecular basis of spatial lipid phosphate signaling

Bioactive lipid phosphates, such as lysophosphatidic acid (LPA) and sphingosine-1-phosphate, are potent membrane-embedded signals that regulate fundamental processes in development, immunity, and cancer. The termination of these signals is mediated by phospholipid phosphatases (PLPPs), yet the molecular principles governing their function at the membrane interface have remained poorly understood. Here we report high-resolution cryo-electron microscopy structures of human PLPP1 in apo (1.87 Å) and product-bound (2.21 Å) states. The structures reveal a highly ordered, C4-symmetric homotetramer with ordered lipid densities—including densities assigned to phosphatidylcholine, phosphatidic acid, and phosphatidylinositol-4,5-bisphosphate—at inter-subunit interfaces. Structure-guided mutagenesis shows that residues surrounding these interfacial lipid densities affect enzymatic activity, whereas oligomerization analysis indicates that activity loss does not simply correlate with tetramer disruption. The product-bound structure defines the catalytic pocket and a membrane-facing tunnel that suggests a possible route for LPA access, while electrophysiological recordings detected no PLPP1-associated ion conductance under the conditions tested. Together, these findings provide a structural framework for PLPP1 tetramer assembly, lipid phosphate hydrolysis, and product recognition. Lipid phosphate phosphatases regulate bioactive lipids involved in cell signalling. Here, the authors reveal how human PLPP1 assembles and recognizes lipids, providing a structural framework for its membrane-associated activity.