4ATV

STRUCTURE OF A TRIPLE MUTANT OF THE NHAA DIMER, CRYSTALLISED AT LOW PH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.287 
  • R-Value Observed: 0.288 

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:  
    4AU5, 4ATV

  • 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 Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE, England, UK Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, Oxford, Didcot, Oxfordshire OX11 0FA, England, UK School of Life Sciences, University of Warwick, Coventry CV4 7AL, England, UK obeckste@asu.edu ddrew@dbb.su.se a.cameron@warwick.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NA(+)/H(+) ANTIPORTER NHAAABCD401Escherichia coliMutation(s): 3 
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Antiporters
Protein: 
NhaA Na+/H+ antiporter in dimeric state (inward-facing)
Find proteins for P13738 (Escherichia coli (strain K12))
Explore P13738 
Go to UniProtKB:  P13738
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LMU
Query on LMU

Download CCD File 
B
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,B,C,DL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.287 
  • R-Value Observed: 0.288 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.76α = 90
b = 99.4β = 97.35
c = 140.23γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2015-07-29
    Changes: Database references
  • Version 1.2: 2018-01-17
    Changes: Database references