Sandbox Reserved 1600: Difference between revisions

One potential proton pathway is formed from the <scene name='83/838655/Bdoxidase_helix_a_1-4/1'>four-helix bundle (a1-4)</scene> of <scene name='83/838655/Bdoxidase_cyda_subunit/2'>CydA</scene>. It is called the <scene name='83/838655/Bdoxidase_cyda_pathway_glu108/1'>CydA pathway</scene>. The residues along this pathway help facilitate the movement of the protons. The location of <scene name='83/838655/Bdoxidase_cyda_pathway_glu108/2'>Glu108</scene> in the structure is a key residue in this pathway. Its location within the pathway and negative charge characteristic implies that this [https://en.wikipedia.org/wiki/Glutamic_acid glutamate] residue is a redox state-dependent mediator of proton transfer. In other words, it acts like a proton shuttle.<ref name =”Safarian” /> The <scene name='83/838655/Bdoxidase_cyda_pathway_glu101/1'>Glu101 residue</scene>, which is the last residue in this pathway, could be the protonatable group eventually used upon <scene name='83/838655/Bd_oxidase_heme_b_595/1'>Heme B595</scene> reduction. More research needs to be done to determine whether the CydA pathway is solely providing protons for charge compensation, or whether <scene name='83/838655/Bdoxidase_cyda_pathway_glu108/2'>Glu108</scene> can be a branching point that is able to pass protons via the <scene name='83/838655/Bd_oxidase_heme_b_595/1'>Heme B595</scene> propionates to the oxygen-binding site.<ref name=”Safarian”>PMID:27126043</ref>

As mentioned above, the purpose of the bd oxidase is to reduce O₂ to 2H₂O using quinol as the reducing substrate, and having the overall reaction of O₂ + 4H⁺ + 4e^- → 2H₂O. The oxygen comes from the extracellular side of the protein, and enters through the oxygen entry site to <scene name='83/838655/Bd_oxidase_heme_d/1'>Heme D</scene>. This pathway is depicted in <font color='orange'><b>orange</b></font> in Figure 4.

The protons that are required in the pathway are not provided by a pump, but rather via intracellular water. The <scene name='83/838655/Bdoxidase_proton_pathways/1'>potential proton pathways</scene> utilize amino acids with charges that help shuttle the protons from the intracellular side of the protein to <scene name='83/838655/Bd_oxidase_heme_b_595/1'>Heme B595</scene>. in the active site. The <scene name='83/838655/Bdoxidase_cyda_pathway_glu108/1'>CydA pathway</scene> passes through the <scene name='83/838655/Bdoxidase_cyda_subunit/2'>CydA subunit</scene>, and is shown in <font color='purple'><b>purple</b></font> in Figure 4. The <scene name='83/838655/Bdoxidase_cydb_pathway/3'>CydB pathway</scene> proceeds through the <scene name='83/838655/Bdoxidase_cydb_subunit/2'>CydB subunit</scene>, and is shown in <font color='green'><b>green</b></font> in Figure 4.

As shown above, the electrons required for the reduction mechanism come from a ubiquinol molecule (Fig. 2) that simultaneously binds to the <scene name='83/838655/Bdoxidase_q_loop/2'>Q loop</scene> and gets oxidized giving 4e^- to <scene name='83/838655/Bd_oxidase_heme_558/2'>Heme B558</scene>. Once at <scene name='83/838655/Bd_oxidase_heme_558/2'>Heme B558</scene> the 4e^- will be shuttled directly to <scene name='83/838655/Bd_oxidase_heme_d/1'>Heme D</scene> to be used in the reduction of O₂. The electron pathway is depicted in <font color='blue'><b>blue</b></font> in Figure 4.

When all of these elements of the reduction aggregate in the active site, the protons and electrons are shuttled to <scene name='83/838655/Bd_oxidase_heme_d/1'>Heme D</scene>, where the actual reduction occurs. The 2H₂O molecules are then expelled, as seen in <font color='red'><b>red</b></font> in Figure 4. The shuttling of these electrons and protons also helps assist with the electric chemical potential in the [https://en.wikipedia.org/wiki/Cell_membrane cellular membrane].