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

Iven Winkelmann, Povilas Uzdavinys, Ian M. Kenney, Joseph Brock, Pascal F. Meier, Lina Marie Wagner, Florian Gabriel, Sukkyeong Jung, Rei Matsuoka, Christoph von Ballmoos, Oliver Beckstein*, David Drew*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

15 Citations (Scopus)

Abstract

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.

Original languageEnglish
Article number6383
JournalNature Communications
Volume13
Issue number1
DOIs
Publication statusPublished - Dec 2022

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