The notorious difficulty of elucidating structures of membrane transporters by crystallography has long prevented our understanding of active transport mechanism coupled with ion/proton transport. The determination of the first crystal structure of the drug/H+ antiporter AcrB was a breakthrough for structure-based understanding of drug/H+ antiport. However, although AcrB is a major multidrug exporter in Gram-negative organisms, the majority of bacterial drug exporters are major facilitator superfamily (MFS) drug transporters. As no crystal structures have been solved for MFS transporters, the alternative protein-engineering methods are still very useful for estimating structures and functions of drug/H+ antiporters. This review describes this alternative approach for investigating the structure and function of tetracycline/H+ antiporters.