In Escherichia coli, transport of hexose 6-phosphates is mediated by the P i -linked antiport carrier, UhpT, a member of the major facilitator superfamily. We showed earlier that Lys 391 , a member of an intrahelical salt bridge (Asp 388 /Lys 391 ) in the eleventh transmembrane segment (TM11) of this transporter, can function as a determinant of substrate selectivity (Hall, J. A., Fann, M.-C., and Maloney, P. C. (1999) J. Biol. Chem. 274, 6148 -6153). Here, we examine in detail the role of TM11 in setting substrate preference. Derivatives having an uncompensated cationic charge at either position 388 or 391 (the D388C, D388V, or D388K/K391C variants) are gain-of-function mutants in which phosphoenolpyruvate, not sugar 6-phosphate, is the preferred organic substrate. By contrast, when an uncompensated anionic charge is placed at position 388 (K391C), we observed behavior consistent with an increased preference for monovalent rather than divalent sugar 6-phosphate. Because positions 388 and 391 lie deep within the UhpT hydrophobic sector, these findings suggested that an extended length of TM11 may be accessible to external substrates and probes. To explore this issue, we used a panel of TM11 single cysteine variants to examine the transport of glucose 6-phosphate in the presence and absence of the membrane-impermeant, thiol-reactive agent p-chloromercuribenzosulfonate (PCMBS). Accessibility to PCMBS, together with the pattern of substrate protection against PCMBS inhibition, leads us to conclude that TM11 spans the membrane as an ␣-helix, with approximately two-thirds of its surface lining a substrate translocation pathway. We suggest that this feature is a general property of carrier proteins in the major facilitator superfamily and that for this reason residues in TM11 will serve to carry determinants of substrate selectivity.Secondary transport systems use the chemiosmotic energy generated by the movement of ions down their electrochemical gradients to facilitate the accumulation of small solutes (1-3). The best-studied secondary transporters of this sort belong to the MFS 1 (4, 5), an evolutionarily related collection that accounts for a large fraction of known solute transporters (6). This taxonomic group is comprised of single-polypeptide carriers that show great diversity in both substrate specificity and kinetic mechanism. Despite this heterogeneity, most members of the MFS share a common structural theme, one characterized by the presence of 12 transmembrane segments believed to transverse the membrane in ␣-helical conformation. In select cases, a high preponderance of ␣-helix has been confirmed by circular dichroism or electron spin resonance spectroscopies (7-9). Similar tests suggest that an unrelated transporter, the Na ϩ /H ϩ antiporter, NhaA, also has 12 transmembrane helices, and in this case two-dimensional crystallography has confirmed the inference (10). In no case, however, has the structure of a secondary transporter been solved to a resolution affording molecular analysis.In the absence of d...