Structure and elevator mechanism of the mammalian sodium/proton exchanger NHE9. (29th October 2020)

• Record Type: Journal Article
• Authors: Winkelmann, Iven; Matsuoka, Rei; Meier, Pascal F; Shutin, Denis; Zhang, Chenou; Orellana, Laura; Sexton, Ricky; Landreh, Michael; Robinson, Carol V; Beckstein, Oliver; Drew, David
• Is Part Of: EMBO journal. Volume 39:Number 24(2020)
• Page Start: 4541
• Page End: 4559
• Publication Date: 2020-10-29
• Subjects: membrane protein -- SLCA9 -- pH regulation -- sodium/proton exchanger -- structure; Molecular biology -- Periodicals; 572.805
• DOI: 10.15252/embj.2020105908
• Languages: English
• ISSNs: 0261-4189

Abstract

Abstract: Na + /H + exchangers (NHEs) are ancient membrane‐bound nanomachines that work to regulate intracellular pH, sodium levels and cell volume. NHE activities contribute to the control of the cell cycle, cell proliferation, cell migration and vesicle trafficking. NHE dysfunction has been linked to many diseases, and they are targets of pharmaceutical drugs. Despite their fundamental importance to cell homeostasis and human physiology, structural information for the mammalian NHEs was lacking. Here, we report the cryogenic electron microscopy structure of NHE isoform 9 (SLC9A9) from Equus caballus at 3.2 Å resolution, an endosomal isoform highly expressed in the brain and associated with autism spectrum (ASD) and attention deficit hyperactivity (ADHD) disorders. Despite low sequence identity, the NHE9 architecture and ion‐binding site are remarkably most similar to distantly related bacterial Na + /H + antiporters with 13 transmembrane segments. Collectively, we reveal the conserved architecture of the NHE ion‐binding site, their elevator‐like structural transitions, the functional implications of autism disease mutations and the role of phosphoinositide lipids to promote homodimerization that, together, have important physiological ramifications. Synopsis: Exchange of sodium for protons across cell membranes regulates intracellular pH and cell volume. Here, cryo‐EM combined with functional assays provides first insights into the structure and membrane context of a mammalian Na + /H + exchanger (NHE). The Equus caballus NHE9/SLC9A9 monomer comprises 13 transmembrane segments and forms a homodimer with similar topology as bacterial antiporter homologues. The NHE9 structure at 3.2 Å shows an inward‐facing conformation, with a highly conserved Na + ‐binding site. Functional assays suggest stabilization of the NHE9 homodimer by phosphoinositide lipid binding to an extracellular loop domain. Autism‐associated disease mutants map onto highly flexible regions in NHE9, likely impairing endosomal pH regulation by NHE9. Intrinsic NHE9 dynamics support an elevator‐like alternating access mechanism in mammalian Na + /H + exchange. Abstract : Cryo‐EM structures reveal conserved architecture and exchange mechanism of the horse endosomal Na + /H + exchanger NHE9.