Sandbox Reserved 1600: Difference between revisions
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[[Image:Hemes2.png|300 px|right|thumb|Figure 1. The active site of bd oxidase for ''Geobacillus thermodenitrificans''. Heme B558 (pink; left), Heme B595 (pink; right), and Heme D (green). Important residues shown in blue. Measurements are shown in Å.]] | [[Image:Hemes2.png|300 px|right|thumb|Figure 1. The active site of bd oxidase for ''Geobacillus thermodenitrificans''. Heme B558 (pink; left), Heme B595 (pink; right), and Heme D (green). Important residues shown in blue. Measurements are shown in Å.]] | ||
The active site for bd oxidase in '' | The active site for bd oxidase in ''G. thermodenitrificans'' is located in subunit Cyd A. The site consists of three iron hemes: <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene>, <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene>, and <scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene> that are held together in a rigid triangular <scene name='83/838655/Hemes/8'>arrangement</scene> due to [https://en.wikipedia.org/wiki/Van_der_Waals_force Van der Waals interactions].<ref name = ”Safarian” /> The <scene name='83/838655/Hemes_measurements/5'>length</scene> between each heme's central iron is relatively constant which serves to shuttle protons and electrons from one heme to another efficiently (Fig. 1). <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene> is hypothesized to act as an electron acceptor, orientated toward the extracellular side by <scene name='83/838655/Bdoxidase_structure_heme/4'>His 186, Met 325, and Lys 252</scene> (Fig. 1).<ref name = ”Safarian” /> With <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene> closest in proximity to the intracellular side, Heme B559 is likely the proton acceptor with two potential proton pathways. Both <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene> and <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene> then shuttle their respective ions directly to <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene> as this is the shortest pathway. | ||
==Potential Oxygen Entry Site== | ==Potential Oxygen Entry Site== | ||
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==Electron Source== | ==Electron Source== | ||
An electron source is needed in order for the redox reaction of O₂ to occur. Cytochrome bd oxidase uses the quinol molecule [https://en.wikipedia.org/wiki/Coenzyme_Q10 ubiquinone] as an electron donor | An electron source is needed in order for the redox reaction of O₂ to occur. Cytochrome bd oxidase uses the quinol molecule [https://en.wikipedia.org/wiki/Coenzyme_Q10 ubiquinone] as an electron donor. [[Image:Ubiquinone.jpg|200 px|right|thumb|Figure 2. Chemical structure of ubiquinone.]] As shown in the <scene name='83/838655/Bdoxidase_structure_full/4'>overall structure</scene> the <scene name='83/838655/Bdoxidase_q_loop/2'>Q loop</scene> is on the extracellular surface and provides a binding site for ubiquinone.<ref name = ”Safarian” /> As mentioned in the Active Site section, Heme <scene name='83/838655/Bdoxidase_qloop_zoom/3'>B558 is closest in proximity to the Q loop</scene> and thus is the suggested [https://en.wikipedia.org/wiki/Electron_acceptor electron acceptor]. This suggestion is further supported by the conservation of <scene name='83/838655/Bdoxidase_trp/2'>Trp374</scene> often found as intermediate electron receptors in biological [https://en.wikipedia.org/wiki/Electron_transport_chain electron transfer chains].<ref name =”Safarian” /> | ||
==Potential Proton Pathways== | ==Potential Proton Pathways== | ||
