7S24

Crystal structure of the Na+/H+ antiporter NhaA at pH 6.5

Summary for 7S24

• Entry DOI: 10.2210/pdb7s24/pdb
• Descriptor: Na(+)/H(+) antiporter NhaA, PENTAETHYLENE GLYCOL, (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, ... (4 entities in total)
• Functional Keywords: transport protein
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 43255.78

Authors

Drew, D.,Brock, J.,Uzdavinys, P.,Matsuoka, R. (deposition date: 2021-09-03, release date: 2022-08-10, Last modification date: 2023-10-25)

Primary citation

Winkelmann, I.,Uzdavinys, P.,Kenney, I.M.,Brock, J.,Meier, P.F.,Wagner, L.M.,Gabriel, F.,Jung, S.,Matsuoka, R.,von Ballmoos, C.,Beckstein, O.,Drew, D.
Crystal structure of the Na + /H + antiporter NhaA at active pH reveals the mechanistic basis for pH sensing.
Nat Commun, 13:6383-6383, 2022

PubMed Abstract: The strict exchange of protons for sodium ions across cell membranes by NaH 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.

PubMed: 36289233
DOI: 10.1038/s41467-022-34120-z

Experimental method

X-RAY DIFFRACTION (2.2 Å)