CaCAs are integral membrane proteins containing 10-11 predicted transmembrane helices (TMs) (1) (SI Appendix, Fig. S1). Despite the divergence in cation driving force, the superfamily is defined by the presence of two highly conserved α-repeat motifs in TMs 2-3 (α-1) and TMs 7-8 (α-2). The importance of these conserved motifs for Ca 2+ /cation exchange has been well documented in all characterized CaCA proteins (8-10), implying the conservation of the Ca 2+ /cation translocation mechanism in the CaCA superfamily. Recently, Liao et al. reported the crystal structure of the NCX_Mj protein (6). The structure shows a large cavity opening on the periplasmic surface (outward-facing conformation) with both Ca 2+ and Na + bound at the α-repeat regions, suggesting the following hypotheses: (i) a substrate alternating access mechanism in which Ca 2+ and the counter transported cation access the ion-binding sites from each side of the membrane surface; and (ii) transition between outward-facing and inward-facing conformations is required to achieve Ca 2+ /cation exchange. Although the structure of the outward-facing conformation of NCX_Mj is available, structural evidence for the conformational change essential for alternating substrate access has not yet been obtained for any CaCA member. In addition, how the CaCA superfamily proteins modify their Ca 2+ -translocation pathways to use the different cation-gradient driving forces, H + vs. Na + , remains a fundamental and interesting question.To address these important questions, here, we report the crystal structure of an inward-facing conformation of the YfkE protein. This structure, together with protein kinetic analysis, not only provides an important structural characterization of the mechanism of Ca 2+ efflux across the cell membrane but also sheds light on the different modes of energy coupling used by members of the CaCA protein superfamily.
Results
Ca
2+-Transport Specificity and Structural Determination of YfkE.
YfkE catalyzes a H+ -coupled Ca 2+ influx in everted vesicles (SI Appendix, Fig. S2A This article is a PNAS Direct Submission.Data deposition: The atomic coordinates and structure factors have been deposited in the Protein Data Bank, www.pdb.org (PDB ID codes 4KJR and 4KJS).