PDBsum entry 4kjs

Transport protein

PDB id: 4kjs

Contents

Protein chains

320 a.a.

Waters ×18

PDB id:

4kjs

Name:

Transport protein

Title:

Structure of native yfke

Structure:

Cation exchanger yfke. Chain: a, b. Engineered: yes

Source:

Bacillus subtilis subsp. Subtilis. Organism_taxid: 224308. Strain: 168. Gene: yfke, bsu07920. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

3.05Å R-factor: 0.219 R-free: 0.262

Authors:

M.Wu,S.Tong,L.Zheng

Key ref:

M.Wu et al. (2013). Crystal structure of Ca2+/H+ antiporter protein YfkE reveals the mechanisms of Ca2+ efflux and its pH regulation. Proc Natl Acad Sci U S A, 110, 11367-11372. PubMed id: 23798403 DOI: 10.1073/pnas.1302515110

Date:

03-May-13 Release date: 26-Jun-13

Protein chains

O34840  (CHAA_BACSU) -  Ca(2+)/H(+) antiporter ChaA from Bacillus subtilis (strain 168)

Seq: 351 a.a.

Struc: 320 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1073/pnas.1302515110

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

PubMed id: 23798403

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

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

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.