Allosteric control of Na ؉ /H ؉ exchange by intracellular protons ensures rapid and accurate regulation of the intracellular pH. Although this allosteric effect was heretofore thought to occur almost instantaneously, we report here the occurrence of a slower secondary activation of the epithelial Na ؉ /H ؉ exchanger (NHE)-3 isoform. This slow activation mode developed over the course of minutes and was unique to NHE3 and the closely related isoform NHE5, but was not observed in NHE1 or NHE2. Activation of NHE3 was not due to increased density of exchangers at the cell surface, nor was it accompanied by detectable changes in phosphorylation. The association of NHE3 with the cytoskeleton, assessed by its retention in the detergent-insoluble fraction, was similarly unaffected by acidification. In contrast to the slow progressive activation elicited by acidification, deactivation occurred very rapidly upon restoration of the physiological pH. We propose that NHE3 undergoes a slow pH-dependent transition from a less active to a more active state, likely by changing its conformation or state of association. Na ϩ /H ϩ exchangers (NHEs) 1 catalyze the electroneutral counter-transport of Na ϩ for H ϩ across biological membranes (for review, see Refs. 1-3). To date, seven different NHE isoforms have been cloned, all of which are integral membrane proteins with multiple transmembrane domains and an extensive cytosolic carboxyl-terminal domain. NHE1 and NHE3 are by far the most widely studied isoforms. The former is expressed ubiquitously and, by mediating Na ϩ /H ϩ exchange across the plasma membrane, contributes to the regulation of cytosolic pH and cell volume (2). NHE3 is found in the brush border of epithelial cells in the kidney and gastrointestinal tract and is involved in the transepithelial (re)absorption of NaCl and, indirectly, HCO 3 Ϫ and water (4).Because Na ϩ /H ϩ exchange is electroneutral with a 1:1 stoichiometry, thermodynamic equilibrium is predicted to be attained when [H ϩ where K e is the equilibrium constant and the subscripts i and o refer to intraand extracellular, respectively (5). In almost all cells, a steep inwardly directed Na ϩ gradient is maintained across the plasma membrane due to extrusion of Na ϩ by the Na ϩ /K ϩ -ATPase. Based on the concentrations recorded in most cases ([Na ϩ ] o being at least 10 times higher than [Na ϩ ] i ), it is apparent that NHE could drive the intracellular pH (pH i ) at least 1 unit above the external pH. Nevertheless, pH i rarely exceeds and is usually lower than the extracellular pH because NHE becomes virtually quiescent at pH i Ն7.2. This behavior has been attributed to the existence of an allosteric pH-sensitive site on the cytosolic aspect of NHE. The set point at which quiescence is dictated by this allosteric or "modifier" site is presumably intended to stabilize pH i near the physiological optimum level and to preclude deleterious alkalinization (6, 7).Although little is known about the molecular identity of the modifier site, the pH dependence of acti...