Sandbox Reserved 1069: Difference between revisions
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=== Zinc Binding Sites === | === Zinc Binding Sites === | ||
[[Image:full_view.png|thumb|left|]] | [[Image:full_view.png|thumb|left|]] | ||
Each zinc promoter contains three zinc binding sites. There is an active site (Site A), and two cytoplasmic binding sites (Site B and C). It was found that only site A and C are conserved, while Site B | Each zinc promoter contains three zinc binding sites. There is an active site (Site A), and two cytoplasmic binding sites (Site B and C). It was found that only site A and C are conserved, while the function of Site B is still unknown, though it seems to play a role in subunit dimerization. | ||
'''Binding Site A''' | '''Binding Site A''' | ||
Binding site A is in the center of the transmembrane domain, attached and confined via residues from the TM2 and TM5 helices. The TM2 domain has Asp45 and Asp49, and the TM5 has His153 and Asp157. This site is the protein's active site, meaning that this is where the zinc is able to attach and eventually exit the cell via proton transport. This particular site has an ideal tetrahedron among its residues which is preferred for zinc, thus making it the perfect active site for zinc to bind. | Binding site A is in the center of the transmembrane domain, attached and confined via residues from the TM2 and TM5 helices. The TM2 domain has Asp45 and Asp49, and the TM5 has His153 and Asp157. The TM5 helix is significantly shorter than the other 5 helices around it, and this length forms a cavity in the membrane. In turn, this cavity is able to bind a zinc ion. This site is the protein's active site, meaning that this is where the zinc is able to attach and eventually exit the cell via proton transport. This particular site has an ideal tetrahedron among its residues which is preferred for zinc, thus making it the perfect active site for zinc to bind. | ||
[[Image:Binding_site_A.fw.png|thumb|Binding Site A showing TM2 domain (left) and TM5 domain (right). The Asp45 and Asp49 as well as the His153 and Asp157 are the coordination residues in the acitve site.]] | [[Image:Binding_site_A.fw.png|thumb|Binding Site A showing TM2 domain (left) and TM5 domain (right). The Asp45 and Asp49 as well as the His153 and Asp157 are the coordination residues in the acitve site.]] | ||
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'''Binding Site C''' | '''Binding Site C''' | ||
Binding site C has vastly opposite properties from what is seen in binding site A. It is located on the TM2-TM3 loop on the cytoplasmic membrane and between the two | Binding site C has vastly opposite properties from what is seen in binding site A. It is located on the TM2-TM3 loop on the cytoplasmic membrane and between the two C-terminus domain interfaces. Here, there is a binuclear coordination of zinc between the Asp285 residue that bridges the zinc ions together and the four coordinating residues (His232, His248, His283 and His261). The Asp285 residue is conserved, meaning it does not have outer shell constraints. However, the four histidine residues all have outer shell constraints. These constraints consist of hydrogen bonds to the residues surrounding the binding site. These hydrogen bonds can form bidentate bonds, which means that the hydrogen bond attaches to a metal in two places. These bonds in turn create an extensive network of interactions at the CTD interface, and it is these interactions that allow for stability and strengthening of the CTD-CTD association. | ||
[[Image:binding_site_C_1.png|200px|]][[Image:Bindig_site_c_2.fw.png|200px|]][[Image:Binding_site_c_3.png|200px|]] | [[Image:binding_site_C_1.png|200px|]][[Image:Bindig_site_c_2.fw.png|200px|]][[Image:Binding_site_c_3.png|200px|]] | ||
