Site-directed N-ethylmaleimide labeling was studied with Glu-126 and͞or Arg-144 mutants in lactose permease containing a single, native Cys residue at position 148 in the substrate-binding site. Replacement of either Glu-126 or Arg-144 with Ala markedly decreases Cys-148 reactivity, whereas interchanging the residues, double-Ala replacement, or replacement of Arg-144 with Lys or His does not alter reactivity, indicating that Glu-126 and Arg-144 are charge-paired. Importantly, although alkylation of Cys-148 is blocked by ligand in wild-type permease, no protection whatsoever is observed with any of the Glu-126 or Arg-144 mutants. Site-directed f luorescence with 2-(4-maleimidoanilino)-naphthalene-6-sulfonic acid (MIANS) in mutant Val-331 3 Cys was also studied. In marked contrast to Val-331 3 Cys permease, ligand does not alter MIANS reactivity in mutant Glu-126 3 Ala͞Val-331 3 Cys, Arg-144 3 Ala͞Val-331 3 Cys, or Arg-144 3 Lys͞Val-331 3 Cys and does not cause either quenching or a shift in the emission maximum of the MIANS-labeled mutants. However, mutation Glu-126 3 Ala or Arg-144 3 Ala and, to a lesser extent, Arg-144 3 Lys cause a red-shift in the emission spectrum and render the f luorophore more accessible to I ؊ . The results demonstrate that Glu-126 and Arg-144 are irreplaceable for substrate binding and suggest a model for the substrate-binding site in the permease. In addition, the findings are consistent with the notion that alterations in the substrate translocation pathway at the interface between helices IV and V are transmitted conformationally to the H ؉ translocation pathway at the interface between helices IX and X.The lactose permease (lac permease) of Escherichia coli is representative of secondary active transport proteins that convert free energy stored in electrochemical ion gradients into work in the form of a concentration gradient (reviewed in ref. 1). This hydrophobic, polytopic, cytoplasmic membrane protein catalyzes the coupled stoichiometric translocation of -galactosides and H ϩ . The lacY gene that encodes the permease has been cloned and sequenced, and the product of the lacY gene has been solubilized, purified, reconstituted into proteoliposomes, and shown to be solely responsible for -galactoside transport as a monomer (see ref.2). All available evidence indicates that the permease consists of 12 hydrophobic, membrane-spanning, ␣-helical domains connected by hydrophilic loops with both the N and C termini on the cytoplasmic face of the membrane (Fig. 1) (reviewed in refs. 3 and 4).Site-directed mutagenesis of wild-type permease and Cysscanning mutagenesis of a functional mutant devoid of Cys residues (C-less permease) reveals that 4 of 417 residues in the protein are irreplaceable with respect to coupling between lactose and H ϩ translocation-Glu-269 (helix VIII), Arg-302 (helix IX), His-322 (helix X), and Glu-325 (helix X) (reviewed in refs. 3-5). Although the permease has not been crystallized, application of a battery of site-directed biochemical and biophysical te...