4AU5

Structure of the NhaA dimer, crystallised at low pH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.696 Å
  • R-Value Free: 0.342 
  • R-Value Work: 0.318 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the sodium-proton antiporter NhaA dimer and new mechanistic insights.

Lee, C.Yashiro, S.Dotson, D.L.Uzdavinys, P.Iwata, S.Sansom, M.S.von Ballmoos, C.Beckstein, O.Drew, D.Cameron, A.D.

(2014) J. Gen. Physiol. 144: 529-544

  • DOI: 10.1085/jgp.201411219
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Sodium-proton antiporters rapidly exchange protons and sodium ions across the membrane to regulate intracellular pH, cell volume, and sodium concentration. How ion binding and release is coupled to the conformational changes associated with transport ...

    Sodium-proton antiporters rapidly exchange protons and sodium ions across the membrane to regulate intracellular pH, cell volume, and sodium concentration. How ion binding and release is coupled to the conformational changes associated with transport is not clear. Here, we report a crystal form of the prototypical sodium-proton antiporter NhaA from Escherichia coli in which the protein is seen as a dimer. In this new structure, we observe a salt bridge between an essential aspartic acid (Asp163) and a conserved lysine (Lys300). An equivalent salt bridge is present in the homologous transporter NapA, but not in the only other known crystal structure of NhaA, which provides the foundation of most existing structural models of electrogenic sodium-proton antiport. Molecular dynamics simulations show that the stability of the salt bridge is weakened by sodium ions binding to Asp164 and the neighboring Asp163. This suggests that the transport mechanism involves Asp163 switching between forming a salt bridge with Lys300 and interacting with the sodium ion. pKa calculations suggest that Asp163 is highly unlikely to be protonated when involved in the salt bridge. As it has been previously suggested that Asp163 is one of the two residues through which proton transport occurs, these results have clear implications to the current mechanistic models of sodium-proton antiport in NhaA.


    Organizational Affiliation

    Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, England, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NA(+)/H(+) ANTIPORTER NHAA
A, B, C, D
401Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: nhaA (ant)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Antiporters
Protein: 
NhaA Na+/H+ antiporter
Find proteins for P13738 (Escherichia coli (strain K12))
Go to UniProtKB:  P13738
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
LMU
Query on LMU

Download SDF File 
Download CCD File 
B
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.696 Å
  • R-Value Free: 0.342 
  • R-Value Work: 0.318 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 115.800α = 90.00
b = 100.560β = 97.00
c = 141.612γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2016-01-27
    Type: Database references
  • Version 1.2: 2018-01-17
    Type: Database references