Sandbox Reserved 1600: Difference between revisions

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=Introduction=

<scene name='83/838655/Bdoxidase_structure_full/4'>Cytochrome bd oxidase</scene> is an integral membrane protein that catalyzes the reduction of oxygen to water using quinol as the reducing substrate <ref name=”Giuffrè”>PMID:24486503</ref>. The full reaction is O₂ + 4H+ + 4e- → 2H₂O. The reaction is electrogenic but it is not coupled to a proton pump. Instead, bd oxidase utilizes internal water molecules to provide the four protons needed and an external ~~ubiquinol~~ molecule for the four electrons needed <ref name = ”Safarian”>PMID:31604309</ref>.

<scene name='83/838655/Bdoxidase_structure_full/4'>Cytochrome bd oxidase</scene> is an integral membrane protein that catalyzes the reduction of oxygen to water using quinol as the reducing substrate <ref name=”Giuffrè”>PMID:24486503</ref>. The full reaction is O₂ + 4H+ + 4e- → 2H₂O. The reaction is electrogenic but it is not coupled to a proton pump. Instead, bd oxidase utilizes internal water molecules to provide the four protons needed and an external ubiquinone molecule for the four electrons needed <ref name = ”Safarian”>PMID:31604309</ref>.

There are two main types of respiratory cytochrome oxidases: the heme/copper oxidases, and the heme-only cytochrome bd quinol oxidase, which is what bd oxidase falls under <ref name=”Das”>PMID:15743950</ref>. Heme-only cytochrome bd quinol oxidases are associated with microaerobic dioxygen respiration, and they have a high affinity for oxygen.

There are two main types of respiratory cytochrome oxidases: the heme/copper oxidases and the heme-only cytochrome bd quinol oxidase, which is what bd oxidase falls under <ref name=”Das”>PMID:15743950</ref>. Heme-only cytochrome bd quinol oxidases are associated with microaerobic dioxygen respiration, and they have a high affinity for oxygen.

Cytochrome bd oxidase plays a key role in protecting gram-negative heterotrophs from high oxidative stress (ie. preventing free radicals in intracellular space in prokaryotes) <ref name=”Jünemann”>PMID:9332500</ref>. Other organisms, like humans, have mechanisms that do the same thing but are more intricate due to the organism’s higher levels of complexity.

The ''Geobacillus thermodenitrificans'' organism utilizes the bd oxidase mechanism. The oxygen enters the enzyme through the selective <scene name='83/832926/Potential_oxygen_entry_site/1'>oxygen entry site</scene> that funnels the extracellular oxygen to <scene name='83/838655/Bd_oxidase_heme_d/1'>Heme D</scene> in the active site. The electrons for the reaction are provided by ~~ubiquinol~~ molecule bound to the <scene name='83/838655/Bdoxidase_q_loop/2'>Q loop</scene>. The protons for the reaction are provided by one of two <scene name='83/838655/Bdoxidase_proton_pathways/1'>potential proton pathways</scene>, either the <scene name='83/838655/Bdoxidase_cyda_pathway/6'>CydA pathway</scene>or <scene name='83/838655/Bdoxidase_cydb_pathway/3'>CydB pathway</scene>. Both of the proton pathways utilize the intracellular water molecules for the proton source, and shuttle them to <scene name='83/838655/Bd_oxidase_heme_b_595/1'>Heme B595</scene>.

The ''Geobacillus thermodenitrificans'' organism utilizes the bd oxidase mechanism. The oxygen enters the enzyme through the selective <scene name='83/832926/Potential_oxygen_entry_site/1'>oxygen entry site</scene> that funnels the extracellular oxygen to <scene name='83/838655/Bd_oxidase_heme_d/1'>Heme D</scene> in the active site. The electrons for the reaction are provided by ubiquinone molecule bound to the <scene name='83/838655/Bdoxidase_q_loop/2'>Q loop</scene>. The protons for the reaction are provided by one of two <scene name='83/838655/Bdoxidase_proton_pathways/1'>potential proton pathways</scene>, either the <scene name='83/838655/Bdoxidase_cyda_pathway/6'>CydA pathway</scene>or <scene name='83/838655/Bdoxidase_cydb_pathway/3'>CydB pathway</scene>. Both of the proton pathways utilize the intracellular water molecules for the proton source, and shuttle them to <scene name='83/838655/Bd_oxidase_heme_b_595/1'>Heme B595</scene>.

= Biological Importance of Reducing O₂ =

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==Electron Source==

An electron source is needed in order for the redox reaction of O₂ to occur. Cytochrome bd oxidase uses the quinol molecule ubiquinone as an electron donor. The chemical structure of ubiquinone is shown in Fig. 2. [[Image:Ubiquinone.jpg|200 px|right|thumb|Figure 2. Chemical structure of ubiquinone.]] As ~~shown~~ in the overall <scene name='83/838655/Bdoxidase_qloop/1'>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/2'>B558</scene> is closest in proximity to the Q loop and thus is the suggested electron acceptor. This suggestion is further supported by the conservation of <scene name='83/838655/Trp374/1'>Trp374</scene> often found as intermediate electron receptors in biological electron transfer chains <ref name =”Safarian” />.

An electron source is needed in order for the redox reaction of O₂ to occur. Cytochrome bd oxidase uses the quinol molecule ubiquinone as an electron donor. The chemical structure of ubiquinone is shown in Fig. 2. [[Image:Ubiquinone.jpg|200 px|right|thumb|Figure 2. Chemical structure of ubiquinone.]] As mentioned above, in the overall <scene name='83/838655/Bdoxidase_qloop/1'>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/2'>B558</scene> is closest in proximity to the Q loop and thus is the suggested electron acceptor. This suggestion is further supported by the conservation of <scene name='83/838655/Trp374/1'>Trp374</scene> often found as intermediate electron receptors in biological electron transfer chains <ref name =”Safarian” />.

==Potential Proton Pathways==

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@@ Line 7: / Line 7: @@
 =Introduction=
-<scene name='83/838655/Bdoxidase_structure_full/4'>Cytochrome bd oxidase</scene> is an integral membrane protein that catalyzes the reduction of oxygen to water using quinol as the reducing substrate <ref name=”Giuffrè”>PMID:24486503</ref>. The full reaction is O₂ + 4H<sup>+</sup> + 4e<sup>-</sup> → 2H₂O. The reaction is electrogenic but it is not coupled to a proton pump. Instead, bd oxidase utilizes internal water molecules to provide the four protons needed and an external ubiquinol molecule for the four electrons needed <ref name = ”Safarian”>PMID:31604309</ref>.
+<scene name='83/838655/Bdoxidase_structure_full/4'>Cytochrome bd oxidase</scene> is an integral membrane protein that catalyzes the reduction of oxygen to water using quinol as the reducing substrate <ref name=”Giuffrè”>PMID:24486503</ref>. The full reaction is O₂ + 4H<sup>+</sup> + 4e<sup>-</sup> → 2H₂O. The reaction is electrogenic but it is not coupled to a proton pump. Instead, bd oxidase utilizes internal water molecules to provide the four protons needed and an external ubiquinone molecule for the four electrons needed <ref name = ”Safarian”>PMID:31604309</ref>.
-There are two main types of respiratory cytochrome oxidases: the heme/copper oxidases, and the heme-only cytochrome bd quinol oxidase, which is what bd oxidase falls under <ref name=”Das”>PMID:15743950</ref>. Heme-only cytochrome bd quinol oxidases are associated with microaerobic dioxygen respiration, and they have a high affinity for oxygen.
+There are two main types of respiratory cytochrome oxidases: the heme/copper oxidases and the heme-only cytochrome bd quinol oxidase, which is what bd oxidase falls under <ref name=”Das”>PMID:15743950</ref>. Heme-only cytochrome bd quinol oxidases are associated with microaerobic dioxygen respiration, and they have a high affinity for oxygen.
 Cytochrome bd oxidase plays a key role in protecting gram-negative heterotrophs from high oxidative stress (ie. preventing free radicals in intracellular space in prokaryotes) <ref name=”Jünemann”>PMID:9332500</ref>. Other organisms, like humans, have mechanisms that do the same thing but are more intricate due to the organism’s higher levels of complexity.
-The ''Geobacillus thermodenitrificans'' organism utilizes the bd oxidase mechanism. The oxygen enters the enzyme through the selective <scene name='83/832926/Potential_oxygen_entry_site/1'>oxygen entry site</scene> that funnels the extracellular oxygen to <scene name='83/838655/Bd_oxidase_heme_d/1'>Heme D</scene> in the active site. The electrons for the reaction are provided by ubiquinol molecule bound to the <scene name='83/838655/Bdoxidase_q_loop/2'>Q loop</scene>. The protons for the reaction are provided by one of two <scene name='83/838655/Bdoxidase_proton_pathways/1'>potential proton pathways</scene>, either the <scene name='83/838655/Bdoxidase_cyda_pathway/6'>CydA pathway</scene>or <scene name='83/838655/Bdoxidase_cydb_pathway/3'>CydB pathway</scene>. Both of the proton pathways utilize the intracellular water molecules for the proton source, and shuttle them to <scene name='83/838655/Bd_oxidase_heme_b_595/1'>Heme B595</scene>.
+The ''Geobacillus thermodenitrificans'' organism utilizes the bd oxidase mechanism. The oxygen enters the enzyme through the selective <scene name='83/832926/Potential_oxygen_entry_site/1'>oxygen entry site</scene> that funnels the extracellular oxygen to <scene name='83/838655/Bd_oxidase_heme_d/1'>Heme D</scene> in the active site. The electrons for the reaction are provided by ubiquinone molecule bound to the <scene name='83/838655/Bdoxidase_q_loop/2'>Q loop</scene>. The protons for the reaction are provided by one of two <scene name='83/838655/Bdoxidase_proton_pathways/1'>potential proton pathways</scene>, either the <scene name='83/838655/Bdoxidase_cyda_pathway/6'>CydA pathway</scene>or <scene name='83/838655/Bdoxidase_cydb_pathway/3'>CydB pathway</scene>. Both of the proton pathways utilize the intracellular water molecules for the proton source, and shuttle them to <scene name='83/838655/Bd_oxidase_heme_b_595/1'>Heme B595</scene>.
 = Biological Importance of Reducing O₂ =
@@ Line 35: / Line 35: @@
 ==Electron Source==
-An electron source is needed in order for the redox reaction of O₂ to occur. Cytochrome bd oxidase uses the quinol molecule ubiquinone as an electron donor. The chemical structure of ubiquinone is shown in Fig. 2. [[Image:Ubiquinone.jpg|200 px|right|thumb|Figure 2. Chemical structure of ubiquinone.]] As shown in the overall <scene name='83/838655/Bdoxidase_qloop/1'>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/2'>B558</scene> is closest in proximity to the Q loop and thus is the suggested electron acceptor. This suggestion is further supported by the conservation of <scene name='83/838655/Trp374/1'>Trp374</scene> often found as intermediate electron receptors in biological electron transfer chains <ref name =”Safarian” />.
+An electron source is needed in order for the redox reaction of O₂ to occur. Cytochrome bd oxidase uses the quinol molecule ubiquinone as an electron donor. The chemical structure of ubiquinone is shown in Fig. 2. [[Image:Ubiquinone.jpg|200 px|right|thumb|Figure 2. Chemical structure of ubiquinone.]] As mentioned above, in the overall <scene name='83/838655/Bdoxidase_qloop/1'>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/2'>B558</scene> is closest in proximity to the Q loop and thus is the suggested electron acceptor. This suggestion is further supported by the conservation of <scene name='83/838655/Trp374/1'>Trp374</scene> often found as intermediate electron receptors in biological electron transfer chains <ref name =”Safarian” />.
 ==Potential Proton Pathways==