Mechanistic studies of the human NIPA2 transporter

The Non-Imprinted in Prader-Willi/Angelman syndrome 2 (NIPA2) is a highly conserved member of the Drug/Metabolite Transporter (DMT) family, originally characterized as a Mg²⁺ transporter. Dysfunction of NIPA2 has been linked to epilepsy and seizures but despite this the molecular mechanisms of transport and substrate recognition, as well as the functional and structural effects of patient mutations. To answer these questions and gain a fundamental understanding of NIPA2, we performed cryo-EM, and liposomal and cell-based assays. Here we show that NIPA2 passively transports both Mg²⁺ and nucleotides, revealing a broader substrate profile than previously appreciated with potential physiological implications. Furthermore, we establish that NIPA2 utilizes an alternating-access mechanism that appears distinct from classical elevator and rocker switch models. Finally, we show that mutation A75T, linked to childhood absence epilepsy, results in loss of function. Our data provides a framework for understanding the physiological role of NIPA2 and related proteins.