EmrE is a multidrug transporter from Escherichia coli that belongs to the Smr family of small multidrug transporters. The secondary structure of EmrE consists of a four helical bundle, as judged by different techniques. EmrE has been extensively characterized; nevertheless, the membrane topology of EmrE has not been determined yet. Previous work with a homologous Smr protein provided partial information of the membrane topology, however the location of the carboxy-terminus remained inconclusive. In this work we probed the membrane topology of EmrE, focusing on the carboxy-terminus of the protein, using two independent approaches. Our results support a secondary structure where the carboxy-terminus faces the cytoplasm, while the first loop faces the periplasm.
