7S24

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

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This is version 1.2 of the entry. See complete history


Literature

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

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.

(2022) Nat Commun 13: 6383-6383

  • DOI: https://doi.org/10.1038/s41467-022-34120-z
  • Primary Citation of Related Structures:  
    7S24

  • PubMed 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.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Na(+)/H(+) antiporter NhaA396Escherichia coliMutation(s): 0 
Gene Names: nhaAnahA
Membrane Entity: Yes 
UniProt
Find proteins for P13738 (Escherichia coli (strain K12))
Explore P13738 
Go to UniProtKB:  P13738
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13738
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.553α = 78.002
b = 47.335β = 67.119
c = 56.392γ = 79.24
Software Package:
Software NamePurpose
MxCuBEdata collection
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--
Knut and Alice Wallenberg FoundationSweden--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)SwedenR01GM118772

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-10
    Type: Initial release
  • Version 1.1: 2023-02-22
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description