Structure and lipid-mediated remodelling mechanism of the Na+/H+ exchanger NHA2

Matsuoka, R.; Fudim, R.; Jung, S.; Zhang, C.; Bazzone, A.; Chatzikyriakidou, Y.; Nomura, N.; Iwata, S.; Orellana, L.; Beckstein, O.; Drew, D.

doi:10.1101/2021.07.22.453398

bioRxiv · 10.1101/2021.07.22.453398

Structure and lipid-mediated remodelling mechanism of the Na+/H+ exchanger NHA2

Matsuoka, R.·Fudim, R.·Jung, S.·Zhang, C.·Bazzone, A.·Chatzikyriakidou, Y.·Nomura, N.·Iwata, S.·Orellana, L.·Beckstein, O.·Drew, D.

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Abstract

Na+/H+ exchangers catalyse an ion-exchange activity that is carried out in most, if not all cells. SLC9B2, also known as NHA2, correlates with the long-sought after sodium/lithium (Na+/Li+) exchanger linked to the pathogenesis of diabetes mellitus and essential hypertension in humans. Despite its functional importance, structural information and the molecular basis of its ion-exchange mechanism have been lacking. Here, we report the cryo EM structures of bison NHA2 in detergent and in nanodiscs at 3.0 and 3.5 [A] resolution, respectively. NHA2 shares closest structural similarity to the bacterial electrogenic Na+/H+ antiporter NapA, rather than other mammalian SLC9A members. Nevertheless, SSM-based electrophysiology results with NHA2 show the catalysis of electroneutral rather than electrogenic ion exchange, and the ion-binding site is quite distinctive, with a tryptophan-arginine- glutamate triad separated from the well-established ion-binding aspartates. These triad residues fine-tune ion binding specificity, as demonstrated by a salt-bridge swap mutant that converts NHA2 into a Li+-specific transporter. Strikingly, an additional N-terminal helix in NHA2 establishes a unique homodimer with a large [~] 25 [A] intracellular gap between protomers. In the presence of phosphatidylinositol lipids, the N-terminal helix rearranges and closes this gap. We confirm that dimerization of NHA2 is required for activity in vivo, and propose that the N- terminal helix has evolved as a lipid-mediated remodelling switch for regulation of transport activity.

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Matsuoka, R., Fudim, R., Jung, S., Zhang, C., Bazzone, A., Chatzikyriakidou, Y., Nomura, N., Iwata, S., Orellana, L., Beckstein, O., Drew, D.. 2021-07-22. Structure and lipid-mediated remodelling mechanism of the Na+/H+ exchanger NHA2. https://doi.org/10.1101/2021.07.22.453398

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