Sandbox Reserved 1066

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Organism

This protein is found in E. coli

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 which is supported 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.

Zn Induced Conformation Change

Conformation changes occur in the TMD and CTD, both of which are heavily influenced by the presence of Zn²⁺.Both of these conformation changes 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 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 act a Zn²⁺ sensor. Using FRET to measure the distance between the CTD of each monomer showed fluorescence quenching as the concentration Zn²⁺ increased. It is not probable that Zn²⁺ bound at site C works it way up to sites A or B, as C binds Zn²⁺ with a much greater affinity.

Allosteric Inhibition

Zn binding to Active Site C causes a conformation change that reduces the affinity for Zn at Active Site A.

Structural highlights

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