Crystal structure of the Na+/H+ antiporter NhaA at active pH reveals the mechanistic basis for pH sensing.

Winkelmann, Iven; Uzdavinys, Povilas; Kenney, Ian M; Brock, Joseph; Meier, Pascal F; Wagner, Lina-Marie; Gabriel, Florian; Jung, Sukkyeong; Matsuoka, Rei; von Ballmoos, Christoph; Beckstein, Oliver; Drew, David (2022). Crystal structure of the Na+/H+ antiporter NhaA at active pH reveals the mechanistic basis for pH sensing. Nature Communications, 13(1), p. 6383. Springer Nature 10.1038/s41467-022-34120-z

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The strict exchange of protons for sodium ions across cell membranes by Na+/H+ exchangers is a fundamental mechanism for cell homeostasis. At active pH, Na+/H+ exchange can be modelled as competition between H+ and Na+ to an ion-binding site, harbouring either one or two aspartic-acid residues. Nevertheless, extensive analysis on the model Na+/H+ antiporter NhaA from Escherichia coli, has shown that residues on the cytoplasmic surface, termed the pH sensor, shifts the pH at which NhaA becomes active. It was unclear how to incorporate the pH senor model into an alternating-access mechanism based on the NhaA structure at inactive pH 4. Here, we report the crystal structure of NhaA at active pH 6.5, and to an improved resolution of 2.2 Å. We show that at pH 6.5, residues in the pH sensor rearrange to form new salt-bridge interactions involving key histidine residues that widen the inward-facing cavity. What we now refer to as a pH gate, triggers a conformational change that enables water and Na+ to access the ion-binding site, as supported by molecular dynamics (MD) simulations. Our work highlights a unique, channel-like switch prior to substrate translocation in a secondary-active transporter.

Item Type:

Journal Article (Original Article)


08 Faculty of Science > Department of Chemistry, Biochemistry and Pharmaceutical Sciences (DCBP)

UniBE Contributor:

von Ballmoos, Christoph


500 Science > 570 Life sciences; biology
500 Science > 540 Chemistry




Springer Nature




Pubmed Import

Date Deposited:

28 Oct 2022 13:58

Last Modified:

05 Dec 2022 16:27

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