Fig. 6

A model for alternating access transport in GkApcT. a Schematic representation of alternating access transport in GkApcT. Starting from an outward facing state the transporter must reside in a conformation that facilitates access of protons, water and amino acid to the binding site. Binding of amino acid causes conformational changes in TM1 and 6 that act to close the extracellular gate. This may be facilitated by water binding to TM1 and movement of F231 that facilitates formation of the occluded state. Further conformational changes are predicted to occur that move the transporter into a fully occluded state, before the intracellular gate starts to open⁴⁶. Our crystal structure likely represents this ‘inward occluded’ state, where the intracellular gate is still present, but held shut through side chain interactions rather than main chain packing. In GkApcT E115 is likely protonated in this state, holding TM6 in close approximation to TM8, where M321 forms part of the intracellular gate. Proton release from E115 causes the water mediated interaction to D237 to break, and TM6 to swing away from TM3 and 8, opening the binding site to the inside of the cell and releasing the bound amino acid and possibly a water molecule. b Structure of GkApcT shown in molecular surface representation with the predicted gating helices shown. Our data suggest that movement of TM6 away from TM3 and 8 opens the binding site to the interior of the cell, and facilitates release of the bound amino acid