Structural basis for PtdInsP2-mediated human TRPML1 regulation

Transient receptor potential mucolipin 1 (TRPML1), a lysosomal channel, maintains the low pH and calcium levels for lysosomal function. Several small molecules modulate TRPML1 activity. ML-SA1, a synthetic agonist, binds to the pore region and phosphatidylinositol-3,5-bisphosphate (PtdIns(3,5)P-2), a natural lipid, stimulates channel activity to a lesser extent than ML-SA1; moreover, PtdIns(4,5)P-2, another natural lipid, prevents TRPML1-mediated calcium release. Notably, PtdIns(3,5)P-2 and ML-SA1 cooperate further increasing calcium efflux. Here we report the structures of human TRPML1 at pH 5.0 with PtdIns(3,5)P-2, PtdIns (4,5)P-2, or ML-SA1 and PtdIns(3,5)P-2, revealing a unique lipid-binding site. PtdIns(3,5)P-2 and PtdIns(4,5)P-2 bind to the extended helices of S1, S2, and S3. The phosphate group of PtdIns (3,5)P-2 induces Y355 to form a pi-cation interaction with R403, moving the S4-S5 linker, thus allosterically activating the channel. Our structures and electrophysiological characterizations reveal an allosteric site and provide molecular insight into how lipids regulate TRP channels.