Sandbox Reserved 1605: Difference between revisions

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Interestingly, the O-channel does not exist in the cytochrome''bd'' oxidase of [https://en.wikipedia.org/wiki/Geobacillus_thermoglucosidasius ''Geobacillus thermodenitrificans'']; instead, oxygen binds directly to the active site<ref name="Safarian2">PMID: 27126043</ref>. The <scene name='83/832931/Cyds/1'>CydS</scene> subunit found in E. coli blocks this alternate oxygen entry site, which allows oxygen to travel through the O-channel<ref name="Safarian">PMID:31604309</ref><ref name="Alexander">PMID:31723136</ref>. The presence of an o-channel affects oxidase activity, as the ''E. coli'' oxidase acts as a "true" oxidase, while the ''G. thermodenitrificans'' bd oxidase contributes more to detoxification<ref name="Alexander">PMID:31723136</ref>.

=== Hemes ===

Three <scene name='83/832931/Heme/6'>hemes</scene> are present in the CydA subunit. These three hemes form a triangle to maximize subunit stability<ref name="Safarian">PMID:31604309</ref><ref name="Alexander">PMID:31723136</ref><ref name="Safarian2">PMID:27126043</ref>, which is an evolutionary conserved feature across bd oxidases<ref name="Safarian">PMID:31604309</ref>. Heme b558 acts as the primary electron acceptor by catalyzing the oxidation of quinol<ref name="Alexander">PMID:31723136</ref>. Conserved <scene name='83/832931/Met393/1'>His186 and Met393</scene> help to stabilize heme b558<ref name="Alexander">PMID:31723136</ref>. Heme b558 transfers the electrons to heme b595, which transfers them to the active site heme d<ref name= "Safarian">PMID:31604309</ref>. A conserved <scene name='83/832931/Trp441/5'>Trp441</scene> assists heme b595 in transferring electrons to heme d<ref name="Safarian2">PMID:27126043</ref>. A conserved <scene name='83/832931/Hemeb595/2'>Glu445</scene> is essential for charge stabilization of heme b595<ref name="Alexander">PMID:31723136</ref>, while <scene name='83/832931/Hemeh19/2'>His19</scene> stabilizes heme d<ref name="Safarian2">PMID:27126043</ref>. As heme d collects the electrons from heme b595, <scene name='83/832931/Heme_d/3'>Glu99</scene> in the O-channel facilities the binding of oxygen to heme d, and <scene name='83/832931/Heme_d/3'>Ser108, Glu107, and Ser140</scene> in the h-channel facilitate proton transfer to heme d<ref name="Safarian">PMID:31604309</ref>. Similar to the three hemes, the <scene name='83/832931/Uq8/3'>ubiquinone-8</scene> (UQ-8) molecule found in CydB mimics the triangular formation to stabilize the subunit<ref name="Safarian">PMID:31604309</ref>.

Three <scene name='83/832931/Heme/6'>hemes</scene> are present in the CydA subunit. These three hemes form a triangle to maximize subunit stability<ref name="Safarian">PMID:31604309</ref><ref name="Alexander">PMID:31723136</ref><ref name="Safarian2">PMID:27126043</ref>, which is an evolutionary conserved feature across bd oxidases<ref name="Safarian">PMID:31604309</ref>. Heme b558 acts as the primary electron acceptor by catalyzing the oxidation of quinol<ref name="Alexander">PMID:31723136</ref>. Conserved <scene name='83/832931/Met393/1'>His186 and Met393</scene> help to stabilize heme b558<ref name="Alexander">PMID:31723136</ref>. Heme b558 transfers the electrons to heme b595, which transfers them to the active site heme d<ref name= "Safarian">PMID:31604309</ref>. A conserved <scene name='83/832931/Trp441/6'>Trp441</scene> assists heme b595 in transferring electrons to heme d<ref name="Safarian2">PMID:27126043</ref>. A conserved <scene name='83/832931/Hemeb595/2'>Glu445</scene> is essential for charge stabilization of heme b595<ref name="Alexander">PMID:31723136</ref>, while <scene name='83/832931/Hemeh19/3'>His19</scene> stabilizes heme d<ref name="Safarian2">PMID:27126043</ref>. As heme d collects the electrons from heme b595, <scene name='83/832931/Heme_d/3'>Glu99</scene> in the O-channel facilities the binding of oxygen to heme d, and <scene name='83/832931/Heme_d/3'>Ser108, Glu107, and Ser140</scene> in the h-channel facilitate proton transfer to heme d<ref name="Safarian">PMID:31604309</ref>. Similar to the three hemes, the <scene name='83/832931/Uq8/3'>ubiquinone-8</scene> (UQ-8) molecule found in CydB mimics the triangular formation to stabilize the subunit<ref name="Safarian">PMID:31604309</ref>.

===Mechanism===

Quinol is used as the initial electron donor and heme b558 is the initial electron acceptor. <scene name='83/832931/Heme/6'>Heme b558</scene> transfers the electrons to <scene name='83/832931/Heme/6'>heme b595</scene>, which transfers the electrons to <scene name='83/832931/Heme/6'>heme d</scene>. Concurrently, the <scene name='83/832931/Overall_h_channel/1'>H-channel</scene> will collect protons and <scene name='83/832931/O_channel_overall/2'>o-channel</scene> will collect oxygen atoms that will flow to heme d (Fig. 3). With electrons, oxygen, and protons available, heme d can successfully reduce dioxygen to water (Fig. 4).

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 Interestingly, the O-channel does not exist in the cytochrome''bd'' oxidase of [https://en.wikipedia.org/wiki/Geobacillus_thermoglucosidasius ''Geobacillus thermodenitrificans'']; instead, oxygen binds directly to the active site<ref name="Safarian2">PMID: 27126043</ref>.  The <scene name='83/832931/Cyds/1'>CydS</scene> subunit found in E. coli blocks this alternate oxygen entry site, which allows oxygen to travel through the O-channel<ref name="Safarian">PMID:31604309</ref><ref name="Alexander">PMID:31723136</ref>.  The presence of an o-channel affects oxidase activity, as the ''E. coli'' oxidase acts as a "true" oxidase, while the ''G. thermodenitrificans'' bd oxidase contributes more to detoxification<ref name="Alexander">PMID:31723136</ref>.
 === Hemes ===
-Three <scene name='83/832931/Heme/6'>hemes</scene> are present in the CydA subunit. These three hemes form a triangle to maximize subunit stability<ref name="Safarian">PMID:31604309</ref><ref name="Alexander">PMID:31723136</ref><ref name="Safarian2">PMID:27126043</ref>, which is an evolutionary conserved feature across bd oxidases<ref name="Safarian">PMID:31604309</ref>.  Heme b<sub>558</sub> acts as the primary electron acceptor by catalyzing the oxidation of quinol<ref name="Alexander">PMID:31723136</ref>. Conserved <scene name='83/832931/Met393/1'>His186 and Met393</scene> help to stabilize heme b558<ref name="Alexander">PMID:31723136</ref>. Heme b<sub>558</sub> transfers the electrons to heme b595, which transfers them to the active site heme d<ref name= "Safarian">PMID:31604309</ref>.  A conserved <scene name='83/832931/Trp441/5'>Trp441</scene> assists heme b<sub>595</sub> in transferring electrons to heme d<ref name="Safarian2">PMID:27126043</ref>.  A conserved <scene name='83/832931/Hemeb595/2'>Glu445</scene> is essential for charge stabilization of heme b<sub>595</sub><ref name="Alexander">PMID:31723136</ref>, while <scene name='83/832931/Hemeh19/2'>His19</scene> stabilizes heme d<ref name="Safarian2">PMID:27126043</ref>. As heme d collects the electrons from heme b<sub>595</sub>, <scene name='83/832931/Heme_d/3'>Glu99</scene> in the O-channel facilities the binding of oxygen to heme d, and <scene name='83/832931/Heme_d/3'>Ser108, Glu107, and Ser140</scene> in the h-channel facilitate proton transfer to heme d<ref name="Safarian">PMID:31604309</ref>. Similar to the three hemes, the <scene name='83/832931/Uq8/3'>ubiquinone-8</scene> (UQ-8) molecule found in CydB mimics the triangular formation to stabilize the subunit<ref name="Safarian">PMID:31604309</ref>.
+Three <scene name='83/832931/Heme/6'>hemes</scene> are present in the CydA subunit. These three hemes form a triangle to maximize subunit stability<ref name="Safarian">PMID:31604309</ref><ref name="Alexander">PMID:31723136</ref><ref name="Safarian2">PMID:27126043</ref>, which is an evolutionary conserved feature across bd oxidases<ref name="Safarian">PMID:31604309</ref>.  Heme b<sub>558</sub> acts as the primary electron acceptor by catalyzing the oxidation of quinol<ref name="Alexander">PMID:31723136</ref>. Conserved <scene name='83/832931/Met393/1'>His186 and Met393</scene> help to stabilize heme b558<ref name="Alexander">PMID:31723136</ref>. Heme b<sub>558</sub> transfers the electrons to heme b595, which transfers them to the active site heme d<ref name= "Safarian">PMID:31604309</ref>.  A conserved <scene name='83/832931/Trp441/6'>Trp441</scene> assists heme b<sub>595</sub> in transferring electrons to heme d<ref name="Safarian2">PMID:27126043</ref>.  A conserved <scene name='83/832931/Hemeb595/2'>Glu445</scene> is essential for charge stabilization of heme b<sub>595</sub><ref name="Alexander">PMID:31723136</ref>, while <scene name='83/832931/Hemeh19/3'>His19</scene> stabilizes heme d<ref name="Safarian2">PMID:27126043</ref>. As heme d collects the electrons from heme b<sub>595</sub>, <scene name='83/832931/Heme_d/3'>Glu99</scene> in the O-channel facilities the binding of oxygen to heme d, and <scene name='83/832931/Heme_d/3'>Ser108, Glu107, and Ser140</scene> in the h-channel facilitate proton transfer to heme d<ref name="Safarian">PMID:31604309</ref>. Similar to the three hemes, the <scene name='83/832931/Uq8/3'>ubiquinone-8</scene> (UQ-8) molecule found in CydB mimics the triangular formation to stabilize the subunit<ref name="Safarian">PMID:31604309</ref>.
 ===Mechanism===
 Quinol is used as the initial electron donor  and heme b<sub>558</sub> is the initial electron acceptor.  <scene name='83/832931/Heme/6'>Heme b<sub>558</sub></scene> transfers the electrons to <scene name='83/832931/Heme/6'>heme b<sub>595</sub></scene>, which transfers the electrons to <scene name='83/832931/Heme/6'>heme d</scene>.  Concurrently, the <scene name='83/832931/Overall_h_channel/1'>H-channel</scene> will collect protons and <scene name='83/832931/O_channel_overall/2'>o-channel</scene> will collect oxygen atoms that will flow to heme d (Fig. 3).  With electrons, oxygen, and protons available, heme d can successfully reduce dioxygen to water (Fig. 4).