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A Conserved Na+ Binding Site of the Sodium-coupled Neutral Amino Acid Transporter 2 (SNAT2)*

The SLC38 family of solute transporters mediates the coupled transport of amino acids and Na+ into or out of cells. The structural basis for this coupled transport process is not known. Here, a profile-based sequence analysis approach was used, predicting a distant relationship with the SLC5/6 transporter families. Homology models using the LeuTAa and Mhp1 transporters of known structure as templates were established, predicting the location of a conserved Na+ binding site in the center of membrane helices 1 and 8. This homology model was tested experimentally in the SLC38 member SNAT2 by analyzing the effect of a mutation to Thr-384, which is predicted to be part of this Na+ binding site. The results show that the T384A mutation not only inhibits the anion leak current, which requires Na+ binding to SNAT2, but also dramatically lowers the Na+ affinity of the transporter. This result is consistent with a previous analysis of the N82A mutant transporter, which has a similar effect on anion leak current and Na+ binding and which is also expected to form part of the Na+ binding site. In contrast, random mutations to other sites in the transporter had little or no effect on Na+ affinity. Our results are consistent with a cation binding site formed by transmembrane helices 1 and 8 that is conserved among the SLC38 transporters as well as among many other bacterial and plant transporter families of unknown structure, which are homologous to SLC38.