We isolated mutants of Escherichia coli HS4006 containing the melibiose-H؉ symporter (MelY) from Enterobacter cloacae that had enhanced fermentation on 1% maltose MacConkey plates. DNA sequencing revealed three site classes of mutations: L-88-P, L-91-P, and A-182-P. The mutants L-88-P and L-91-P had 3.6-and 5.1-fold greater maltose uptake than the wild type and enhanced apparent affinities for maltose. Energycoupled transport was defective for melibiose accumulation, but detectable maltose accumulation for the mutants indicated that active transport is dependent upon the substrate transported through the carrier. We conclude that the residues Leu-88, Leu-91 (transmembrane segment 3 [TMS-3]), and Ala-182 (TMS-6) of MelY mediate sugar selection. These data represent the first MelY mutations that confer changes in sugar selection.The melibiose transporter of Enterobacter cloacae (MelY) is a secondary active transporter and catalyzes the symport (cotransport) of the ␣-galactoside sugar melibiose and cation (22,23). The gene encoding the melibiose transporter, melY, has been cloned, sequenced (22), and found to reside in an inducible operon in the bacterial genome (23). The deduced amino acid sequence of the melY gene has shown a highly hydrophobic protein of 425 residues and 12 predicted transmembrane segments (TMS) (22). Phylogenetic analyses show that the MelY transporter is a member of oligosaccharide H ϩ symporter family 5 and shares highly conserved amino acid sequence motifs with members of the major facilitator superfamily (MFS) (23,24,27,34). MelY is distinct from MelB (27) but shows high sequence identity (22, 23) with the lactose carrier of Escherichia coli (LacY) (7), the raffinose transporter of E. coli (RafB) (1), the sucrose permease of E. coli (CscB) (2, 26), the lactose carrier of Citrobacter freundii (LacY Cf ) (18), and the lactose carrier of Klebsiella pneumoniae (LacY Kp ) (20).Based on multiple sequence and two-dimensional structural analyses of members of the MFS specific for a diverse array of substrates, it has been predicted that the three-dimensional structures of these seemingly distinct transporters are similar (10,11,24,32,33). This suggests that MFS transporters function by a common transport mechanism in which substrate specificities are determined by subtle differences in sequence. The homology shared between LacY and MelY (7,22,27,34) and the differences in substrate selection profiles between them provide a unique opportunity for a comparative study.Shuman and Beckwith first isolated mutants of the E. coli lactose carrier that transport maltose (30). The lactose carrier of E. coli is a well-studied and important model system for the study of secondary active transport, and it consists of an integral membrane protein of 417 amino acids with 12 transmembrane ␣-helices residing in the cytoplasmic membrane (15,16,34). Although the problem of substrate selection has been well documented in LacY (5,6,17,21,29; reviewed in reference 34), it is unknown whether any of its homologs dictate su...