The effect of bulk-phase pH on the apparent affinity (K d app ) of purified wild-type lactose permease (LacY) for sugars was studied. K d app values were determined by ligand-induced changes in the fluorescence of either of two covalently bound fluorescent reporters positioned away from the sugar-binding site. K d app for three different galactopyranosides was determined over a pH range from 5.5 to 11. A remarkably high pK a of Ϸ10.5 was obtained for all sugars. Kinetic data for thiodigalactoside binding measured from pH 6 to 10 show that decreased affinity for sugar at alkaline pH is due specifically to increased reverse rate. A similar effect was also observed with nitrophenylgalactoside by using a direct binding assay. Because affinity for sugar remains constant from pH 5.5 to pH 9.0, it follows that LacY is fully protonated with respect to sugar binding under physiological conditions of pH. The results are consistent with the conclusion that LacY is protonated before sugar binding during lactose/H ؉ symport in either direction across the membrane.lactose permease ͉ membrane transporters ͉ pH titrations ͉ proton translocation ͉ substrate affinity T he lactose permease of Escherichia coli (LacY), a paradigm for the major facilitator superfamily (MFS) of membrane transport proteins (1, 2), translocates a galactosidic sugar and an H ϩ across the cytoplasmic membrane (3, 4). This coupled translocation mechanism enables LacY to use free energy stored in an electrochemical H ϩ gradient (⌬ Hϩ ) to drive sugar accumulation against a concentration gradient (5-7).X-ray crystal structures of LacY (8-10), all of which are in an inward-facing conformation, and a wealth of biochemical/ biophysical data (7, 11-16) provide evidence for an alternatingaccess mechanism of action. By this means, upon sugar binding or imposition of a ⌬ Hϩ ) (interior negative and/or alkaline), the inward-facing cavity closes with opening of an outward-facing cavity, thereby allowing alternative accessibility of the sugarbinding site, which is at the apex of the cavity in the middle of the molecule, to either side of the membrane. A similar model has been proposed for the glycerol phosphate/phosphate antiporter GlpT, a related MFS protein (17) and the ABC transporter Sav 1866 (18). The alternating-access model involves a global conformational change, which is consistent with the highly dynamic nature of LacY (7,13,14,16,(19)(20)(21)(22)(23).A simple kinetic model for lactose/H ϩ symport (Fig. 1) has been proposed based on extensive studies of partial reactions (efflux, equilibrium exchange, and entrance counterflow) catalyzed by LacY and site-directed mutants defective in the symport mechanism (see ref. 5). Wild-type LacY is tightly coupled with respect to sugar and H ϩ translocation and does not translocate H ϩ without substrate or vice versa. The effect of ambient pH on ⌬ Hϩ -driven symport is bell-shaped with an optimum at approximately pH 7.5 (24, 25), whereas the partial reactions exhibit different dependences on pH. For example, rates of lac...