Sandbox Reserved 1625: Difference between revisions
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<StructureSection load='6rx4' size='350' frame='true' side='right' caption='Cartoon representation of E. coli cytochrome bd-1 oxidase designed from [https://www.rcsb.org/structure/6RX4 PDB: 6RX4]. Blue= CydA; green= CydB; yellow= CydX; pink= CydS; gray = hemes and UQ-8.' scene='83/832931/Full/3'> | <StructureSection load='6rx4' size='350' frame='true' side='right' caption='Cartoon representation of E. coli cytochrome bd-1 oxidase designed from [https://www.rcsb.org/structure/6RX4 PDB: 6RX4]. Blue= CydA; green= CydB; yellow= CydX; pink= CydS; gray = hemes and UQ-8.' scene='83/832931/Full/3'> | ||
==Introduction== | ==Introduction== | ||
<scene name='83/832931/Full/4'>Cytochrome bd oxidase</scene> is a type of quinol-dependent transmembrane (Fig. 1) terminal [https://en.wikipedia.org/wiki/Oxidase oxidase] found exclusively in {https://en.wikipedia.org/wiki/Prokaryote prokaryotes].<ref name="Safarian">PMID: 27126043</ref> With a very high oxygen affinity, bd oxidases play a vital role in the [https://en.wikipedia.org/wiki/Oxidative_phosphorylation oxidative phosphorylation] pathway in both gram-positive and gram-negative bacteria. Cytochrome ''bd'' oxidase's responsibility in the oxidative phosphorylation pathway also allows it to act as a key survival factor in the bacterial stress response against antibacterial drugs <ref name="Safarian">PMID: 31604309</ref>, hypoxia, cyanide, [https://en.wikipedia.org/wiki/Nitric_oxide nitric oxide], and H<sub>2</sub>O<sub>2</sub><ref name="Harikishore">PMID: 31939065</ref>. Given this knowledge, ''bd'' oxidases have become an area of scientific research worth pursuing as they could serve as an ideal target for antimicrobial drug development. <ref name="Boot">PMID: 28878275</ref> | <scene name='83/832931/Full/4'>Cytochrome bd oxidase</scene> is a type of quinol-dependent [https://en.wikipedia.org/wiki/Transmembrane_protein transmembrane] (Fig. 1) terminal [https://en.wikipedia.org/wiki/Oxidase oxidase] found exclusively in {https://en.wikipedia.org/wiki/Prokaryote prokaryotes].<ref name="Safarian">PMID: 27126043</ref> With a very high oxygen affinity, bd oxidases play a vital role in the [https://en.wikipedia.org/wiki/Oxidative_phosphorylation oxidative phosphorylation] pathway in both gram-positive and gram-negative bacteria. Cytochrome ''bd'' oxidase's responsibility in the oxidative phosphorylation pathway also allows it to act as a key survival factor in the bacterial stress response against antibacterial drugs <ref name="Safarian">PMID: 31604309</ref>, hypoxia, cyanide, [https://en.wikipedia.org/wiki/Nitric_oxide nitric oxide], and H<sub>2</sub>O<sub>2</sub><ref name="Harikishore">PMID: 31939065</ref>. Given this knowledge, ''bd'' oxidases have become an area of scientific research worth pursuing as they could serve as an ideal target for antimicrobial drug development. <ref name="Boot">PMID: 28878275</ref> | ||
[[Image:Pp_and_cp_of_oxdiase.png|550 px|center|thumb|''Figure 1''. Cartoon model of cytochrome bd-oxidase in ''E. coli''. Dashed lines represent borders of cytoplasmic and periplasmic regions. A bound quinol between transmembrane helices 6 and 7 undergoes oxidation and releases protons into the periplasmic space, generating a proton gradient. Protons and oxygen atoms from the cytoplasmic side enter cytochrome ''bd'' oxidase through specific channels. Oxygen is reduced to water, which is released into the cytoplasmic space. Blue = CydA; green = CydB; yellow = CydX; pink = CydS. [[https://www.rcsb.org/structure/6RX4 PDB: 6RX4]]]] | [[Image:Pp_and_cp_of_oxdiase.png|550 px|center|thumb|''Figure 1''. Cartoon model of cytochrome bd-oxidase in ''E. coli''. Dashed lines represent borders of [https://en.wikipedia.org/wiki/Cytoplasm cytoplasmic] and [https://en.wikipedia.org/wiki/Periplasm periplasmic] regions. A bound quinol between transmembrane helices 6 and 7 undergoes [https://en.wikipedia.org/wiki/Redox oxidation] and releases protons into the periplasmic space, generating a [https://en.wikipedia.org/wiki/Electrochemical_gradient proton gradient]. Protons and oxygen atoms from the cytoplasmic side enter cytochrome ''bd'' oxidase through specific channels. Oxygen is [https://en.wikipedia.org/wiki/Redox reduced] to water, which is released into the cytoplasmic space. Blue = CydA; green = CydB; yellow = CydX; pink = CydS. [[https://www.rcsb.org/structure/6RX4 PDB: 6RX4]]]] | ||
The overall mechanism of ''bd'' oxidases involves an exergonic [https://en.wikipedia.org/wiki/Dioxygen_in_biological_reactions reduction of molecular oxygen] into water (Fig. 2). During this reaction, a proton gradient is generated in order to assist in the conservation of energy. <ref name="Belevich">PMID: 17690093</ref> Unlike other terminal oxidases, bd oxidases do not use a proton pump. Instead, bd oxidases use a form of vectorial chemistry that releases protons from the quinol oxidation into the positive, periplasmic side of the membrane. Protons that are required for the water formation are then consumed from the negative, cytoplasmic side of the membrane, thus creating the previously mentioned proton gradient. | The overall mechanism of ''bd'' oxidases involves an exergonic [https://en.wikipedia.org/wiki/Dioxygen_in_biological_reactions reduction of molecular oxygen] into water (Fig. 2). During this reaction, a proton gradient is generated in order to assist in the conservation of energy. <ref name="Belevich">PMID: 17690093</ref> Unlike other terminal oxidases, bd oxidases do not use a proton pump. Instead, bd oxidases use a form of vectorial chemistry that releases protons from the quinol oxidation into the positive, periplasmic side of the membrane. Protons that are required for the water formation are then consumed from the negative, cytoplasmic side of the membrane, thus creating the previously mentioned proton gradient. | ||
[[Image:proton graadient.jpg|300 px|left|thumb|Figure 2: Overall schematic representation of cytochrome bd oxidase. <ref name= "Giuffre">PMID: 24486503</ref>; General display of the reduction of molecular oxygen into water using the quinol as a reducing substrate. The three hemes are located near the periplasmic space, meaning that the membrane potential is generated mainly from proton transfer from the cytoplasm towards the active site on the opposite site of the membrane. Heme b<sub>558</sub> is involved in quinol oxidation and heme d serves as the site where O2 binds and becomes reduced to H2O.]] | [[Image:proton graadient.jpg|300 px|left|thumb|Figure 2: Overall schematic representation of cytochrome bd oxidase. <ref name= "Giuffre">PMID: 24486503</ref>; General display of the reduction of molecular oxygen into water using the quinol as a reducing substrate. The three hemes are located near the periplasmic space, meaning that the membrane potential is generated mainly from proton transfer from the cytoplasm towards the active site on the opposite site of the membrane. Heme b<sub>558</sub> is involved in quinol oxidation and heme d serves as the site where O2 binds and becomes reduced to H2O.]] | ||
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== Molecular Function == | == Molecular Function == | ||
=== H and O channels === | === H and O channels === | ||
[[Image:O_AND_H_CHANNEL.png|300 px|right|thumb|'''Figure 3'''. H and | [[Image:O_AND_H_CHANNEL.png|300 px|right|thumb|'''Figure 3'''. H and O-channels of cytochrome bd-oxidase in ''E. coli''. Channels are outlined in gray, water is shown as spheres, and relevant amino acids are labeled above. [[https://www.rcsb.org/structure/6RX4 PDB:6RX4]]]] | ||
The hydrogen and oxygen channels (Fig. 3) are essential for H<sup>+</sup> and O<sub>2</sub> molecules to reach the active site of cytochrome ''bd'' oxidase. A [https://en.wikipedia.org/wiki/Chemiosmosis#The_proton-motive_force proton motive force] generated by the oxidase<ref name= "Safarian">PMID:31604309</ref> allows protons from the cytoplasm to flow through a hydrophilic <scene name='83/832931/Overall_h_channel/2'>H-channel</scene> full of water (pink dots), entering at <scene name='83/832931/Start_of_h_channel/2'>Asp119<sup>A</sup></scene> and moving past <scene name='83/832931/Start_of_h_channel/2'>Lys57<sup>A</sup>, Lys109<sup>B</sup>, Asp105<sup>B</sup>, Tyr379<sup>B</sup>, and Asp58<sup>B</sup></scene><ref name="Alexander">PMID:31723136</ref> where they can be transferred to the active site with the help of the conserved residues <scene name='83/832931/End_of_h_channel/4'>Ser108<sup>A</sup>, Glu107<sup>A</sup>, and Ser140<sup>A</sup></scene><ref name= "Safarian">PMID:31604309</ref>. A smaller <scene name='83/832931/O_channel_overall/3'>O-channel</scene> also exists that transitions from hydrophobic to hydrophilic as it gets closer to the active site. This channel allows oxygen to reach the active site, starting near <scene name='83/832931/Ochannel/2'>Trp63</scene> in CydB and passing by <scene name='83/832931/Ochannel/2'>Ile144<sup>A</sup>, Leu101<sup>A</sup>, and Glu99<sup>A</sup></scene><ref name= "Safarian">PMID:31604309</ref>, which assists with the binding of oxygen to the active site. The O-channel channel is approximately 1.5 [https://en.wikipedia.org/wiki/Angstrom Å] in diameter<ref name="Alexander">PMID:31723136</ref>, which may help with [https://en.wikipedia.org/wiki/Chemical_specificity selectivity]. | The hydrogen and oxygen channels (Fig. 3) are essential for H<sup>+</sup> and O<sub>2</sub> molecules to reach the active site of cytochrome ''bd'' oxidase. A [https://en.wikipedia.org/wiki/Chemiosmosis#The_proton-motive_force proton motive force] generated by the oxidase<ref name= "Safarian">PMID:31604309</ref> allows protons from the cytoplasm to flow through a hydrophilic <scene name='83/832931/Overall_h_channel/2'>H-channel</scene> full of water (pink dots), entering at <scene name='83/832931/Start_of_h_channel/2'>Asp119<sup>A</sup></scene> and moving past <scene name='83/832931/Start_of_h_channel/2'>Lys57<sup>A</sup>, Lys109<sup>B</sup>, Asp105<sup>B</sup>, Tyr379<sup>B</sup>, and Asp58<sup>B</sup></scene><ref name="Alexander">PMID:31723136</ref> where they can be transferred to the active site with the help of the conserved residues <scene name='83/832931/End_of_h_channel/4'>Ser108<sup>A</sup>, Glu107<sup>A</sup>, and Ser140<sup>A</sup></scene><ref name= "Safarian">PMID:31604309</ref>. A smaller <scene name='83/832931/O_channel_overall/3'>O-channel</scene> also exists that transitions from hydrophobic to hydrophilic as it gets closer to the active site. This channel allows oxygen to reach the active site, starting near <scene name='83/832931/Ochannel/2'>Trp63</scene> in CydB and passing by <scene name='83/832931/Ochannel/2'>Ile144<sup>A</sup>, Leu101<sup>A</sup>, and Glu99<sup>A</sup></scene><ref name= "Safarian">PMID:31604309</ref>, which assists with the binding of oxygen to the active site. The O-channel channel is approximately 1.5 [https://en.wikipedia.org/wiki/Angstrom Å] in diameter<ref name="Alexander">PMID:31723136</ref>, which may help with [https://en.wikipedia.org/wiki/Chemical_specificity selectivity]. | ||