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Structure

YiiP is a homodimer with transmembrane (TMD) and C-terminal (CTD) domains that are connected via a charge interlocking mechanism located on a flexible loop. There are 3 Zn²⁺ binding sites per unit of homodimer. Site A is located in the TMD, site C is located in the CTD, and site B is located at the junction of the domains join. Both TMD are composed of 6 helices, 4 of which (TM1,TM2,TM4,TM5) form a pore in which Zn²⁺ and H⁺ can reach binding Site A. Zn²⁺ binding at site C helps hold the CTD together and is thought to stabilize conformational changes in YiiP.

Mechanism of Transport

YiiP's ability to export Zn²⁺ from the cytoplasm is best described as an alternating access mechanism with Zn²⁺/H⁺ antiport. YiiP has 2 major structural conformations as shown by the crystallized structures 3H90 and 3J1Z (a YiiP homolog derived from Shewanella oneidensis). 3H90 shows YiiP in its outward-facing conformation and 3J1Z shows the YiiP homolog in an inward-facing conformation. When YiiP is saturated with Zn²⁺ it seems to favor the perplasmic/outward-facing conformation whereas when active sites are either empty or bound to H⁺ the inward facing conformation is favored. This drives the export of Zn²⁺ from the cytoplasm and enhances the coupling of the proton-motive force. Although YiiP exists as a homodimer both monomers can undergo conformation change independent of one other to produce the alternating access mechanism.

Zn²⁺ Induced Conformation Change

Conformation changes occur in the TMD and CTD, both of which are heavily influenced by the presence of Zn²⁺. The conformation change directly involved with Zn²⁺/H⁺ antiport occurs in the TMD as helix pivoting controls what environment site A is available to. Conformation change occurs when the transmembrane helix pairs TM3-TM6 pivot around cation binding site. It is believed that the energy for TMD conformation change comes from energy of binding each substrate. Changing to the outward from the inward-facing conformation causes a shift in TM5 which disrupts the tetrahedral geometry of active site A. This in turn decreases binding affinity site A has for Zn²⁺ and causes Zn²⁺ to leave site A which then favors change back to inward-facing conformation. In contrast the main purpose of conformation change in the CTD is to stabilize the YiiP dimer and acts as a Zn²⁺ sensor. This is possible because of the flexible loop that links the TMD and the CTD. This loop harbors the charge interlock which serves as a hinge that allows movement of the CTD. Using FRET to measure the distance between the CTD of each monomer fluorescence quenching was observed as the concentration Zn²⁺ increased, which supports that idea that Zn²⁺ induces a stabilizing conformation change in the CTD.

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