Structural basis of the transport mechanism of hBGT1.

In the kidney and liver, the betaine/γ-aminobutyric acid (GABA) transporter 1 (BGT1) transports betaine to maintain the osmotic balance of renal medullary cells and reduce the toxicity of homocysteine accumulation. In the brain, BGT1 reuptakes GABA from the synaptic cleft into glial cells to terminate GABAergic signaling. Despite its importance, the molecular mechanisms of BGT1 substrate recognition and ion coupling remain unknown. Here, we resolved the cryo-electron microscopy structures of BGT1 in complex with two substrates, GABA and betaine, as well as the substrate-free form without any fiducial marker. The substrate-bound complex elucidates the mechanism by which BGT1 recognizes chemically distinct GABA and betaine. These structures are trapped in occluded and inward-open states, elucidating the structural basis for conformational transitions. Furthermore, we proposed a Na3-binding site and investigated the functional role of the Na3 site in limiting reverse transport and promoting substrate accumulation. These insights improve our understanding of substrate recognition, conformational transitions, and ion coupling mechanisms in BGT1, as well as other neurotransmitter transporters.