Crystal structure of selenium substituted Ca2+/H+ antiporter proteinYfkE

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 

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Crystal structure of Ca2+/H+ antiporter protein YfkE reveals the mechanisms of Ca2+ efflux and its pH regulation.

Wu, M.Tong, S.Waltersperger, S.Diederichs, K.Wang, M.Zheng, L.

(2013) Proc Natl Acad Sci U S A 110: 11367-11372

  • DOI: https://doi.org/10.1073/pnas.1302515110
  • Primary Citation of Related Structures:  
    4KJR, 4KJS

  • PubMed Abstract: 

    Ca(2+) efflux by Ca(2+) cation antiporter (CaCA) proteins is important for maintenance of Ca(2+) homeostasis across the cell membrane. Recently, the monomeric structure of the prokaryotic Na(+)/Ca(2+) exchanger (NCX) antiporter NCX_Mj protein from Methanococcus jannaschii shows an outward-facing conformation suggesting a hypothesis of alternating substrate access for Ca(2+) efflux. To demonstrate conformational changes essential for the CaCA mechanism, we present the crystal structure of the Ca(2+)/H(+) antiporter protein YfkE from Bacillus subtilis at 3.1-Å resolution. YfkE forms a homotrimer, confirmed by disulfide crosslinking. The protonated state of YfkE exhibits an inward-facing conformation with a large hydrophilic cavity opening to the cytoplasm in each protomer and ending in the middle of the membrane at the Ca(2+)-binding site. A hydrophobic "seal" closes its periplasmic exit. Four conserved α-repeat helices assemble in an X-like conformation to form a Ca(2+)/H(+) exchange pathway. In the Ca(2+)-binding site, two essential glutamate residues exhibit different conformations compared with their counterparts in NCX_Mj, whereas several amino acid substitutions occlude the Na(+)-binding sites. The structural differences between the inward-facing YfkE and the outward-facing NCX_Mj suggest that the conformational transition is triggered by the rotation of the kink angles of transmembrane helices 2 and 7 and is mediated by large conformational changes in their adjacent transmembrane helices 1 and 6. Our structural and mutational analyses not only establish structural bases for mechanisms of Ca(2+)/H(+) exchange and its pH regulation but also shed light on the evolutionary adaptation to different energy modes in the CaCA protein family.

  • Organizational Affiliation

    Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Houston Medical School, Houston, TX 77030, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cation exchanger YfkE
A, B
351Bacillus subtilis subsp. subtilis str. 168Mutation(s): 2 
Gene Names: yfkEBSU07920
Membrane Entity: Yes 
Find proteins for O34840 (Bacillus subtilis (strain 168))
Explore O34840 
Go to UniProtKB:  O34840
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO34840
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.297α = 90
b = 170.297β = 90
c = 95.265γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-03
    Type: Initial release
  • Version 1.1: 2013-08-07
    Changes: Database references