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<scene name='83/832931/Full/4'>Cytochrome bd oxidases</scene> are quinol-dependent [https://en.wikipedia.org/wiki/Transmembrane_protein transmembrane] (Fig. 1) terminal [https://en.wikipedia.org/wiki/Oxidase oxidases] 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>. With their essential roles in bacterial survival, ''bd'' oxidases have been pursued as ideal targets for antimicrobial drug development. <ref name="Boot">PMID: 28878275</ref> | <scene name='83/832931/Full/4'>Cytochrome bd oxidases</scene> are quinol-dependent [https://en.wikipedia.org/wiki/Transmembrane_protein transmembrane] (Fig. 1) terminal [https://en.wikipedia.org/wiki/Oxidase oxidases] 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>. With their essential roles in bacterial survival, ''bd'' oxidases have been pursued as ideal targets for antimicrobial drug development. <ref name="Boot">PMID: 28878275</ref> | ||
[[Image:Transmembrane_bd_ox.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 quinol bound in the periplasmic <scene name='83/832924/Q_loop/3'>Q-loop</scene> is [https://en.wikipedia.org/wiki/Redox oxidized] 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]]]] | [[Image:Transmembrane_bd_ox.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 quinol bound in the periplasmic <scene name='83/832924/Q_loop/3'>Q-loop</scene> is [https://en.wikipedia.org/wiki/Redox oxidized] 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 | 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 proton gradient. | ||
[[Image:proton graadient.jpg|550 px|center|thumb|''Figure 2''. Overall schematic representation of the reductive cycle of cytochrome bd oxidase. <ref name= "Giuffre">PMID: 24486503</ref> In this cycle, molecular oxygen is reduced into water using the quinol as a reducing substrate. Cytochrome ''bd'' oxidase releases 2 H+ for each 2 electrons transferred due to the menaquinol oxidation site located on the outer face of the cytoplasmic membrane. <ref name="Fischer">PMID: 29784883</ref> The ''bd'' oxidase completes a redox loop when coupled with quinone [https://en.wikipedia.org/wiki/Dehydrogenase dehydrogenases] that receive electrons from [https://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH], [https://en.wikipedia.org/wiki/Pyruvic_acid pyruvate], [https://en.wikipedia.org/wiki/Lactic_acid D-lactate], or [https://en.wikipedia.org/wiki/Acyl-CoA acyl coenzyme A]. The three hemes essential to the electron transfer are located near the periplasmic space. Heme b<sub>558</sub> is involved in quinol oxidation and heme d serves as the site where O<sub>2</sub> binds and becomes reduced to H<sub>2</sub>O. The membrane potential is generated mainly from proton transfer from the cytoplasm towards the active site on the periplasmic side of the membrane.]] This page will focus on the structure and overall function of the ''bd'' oxidase in [https://en.wikipedia.org/wiki/Escherichia_coli ''E. coli'']. This ''bd'' oxidase is part of the long(L) quinol-binding domain subfamily of terminal oxidases. The L-subfamily of ''bd'' oxidases are responsible for the survival of acute infectious diseases such as ''E. coli'' and [https://en.wikipedia.org/wiki/Salmonella ''Salmonella'']. The | [[Image:proton graadient.jpg|550 px|center|thumb|''Figure 2''. Overall schematic representation of the reductive cycle of cytochrome bd oxidase. <ref name= "Giuffre">PMID: 24486503</ref> In this cycle, molecular oxygen is reduced into water using the quinol as a reducing substrate. Cytochrome ''bd'' oxidase releases 2 H<sup>+</sup> for each 2 electrons transferred due to the menaquinol oxidation site located on the outer face of the cytoplasmic membrane. <ref name="Fischer">PMID: 29784883</ref> The ''bd'' oxidase completes a redox loop when coupled with quinone [https://en.wikipedia.org/wiki/Dehydrogenase dehydrogenases] that receive electrons from [https://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH], [https://en.wikipedia.org/wiki/Pyruvic_acid pyruvate], [https://en.wikipedia.org/wiki/Lactic_acid D-lactate], or [https://en.wikipedia.org/wiki/Acyl-CoA acyl coenzyme A]. The three hemes essential to the electron transfer are located near the periplasmic space. Heme b<sub>558</sub> is involved in quinol oxidation and heme d serves as the site where O<sub>2</sub> binds and becomes reduced to H<sub>2</sub>O. The membrane potential is generated mainly from proton transfer from the cytoplasm towards the active site on the periplasmic side of the membrane.]] This page will focus on the structure and overall function of the ''bd'' oxidase in [https://en.wikipedia.org/wiki/Escherichia_coli ''E. coli'']. This ''bd'' oxidase is part of the long(L) quinol-binding domain subfamily of terminal oxidases. The L-subfamily of ''bd'' oxidases are responsible for the survival of acute infectious diseases such as ''E. coli'' and [https://en.wikipedia.org/wiki/Salmonella ''Salmonella'']. The cytochrome ''bd'' oxidase's three <scene name='83/832931/Heme/4'>heme</scene> groups, its periplasmically exposed <scene name='83/832924/Q_loop/3'>Q-loop</scene>, and <scene name='83/832942/Four_subunits_labelled_6rx4/3'>four protein subunits</scene> will be the primary focus when explaining how the structure of ''bd'' oxidase allows it to catalyze the reduction of molecular oxygen into water. | ||
==Structure== | ==Structure== | ||
=== Subunits === | === Subunits === | ||
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Three <scene name='83/832931/Heme/6'>hemes</scene> are present in the <scene name='83/832924/Cyda_subunit/6'>CydA subunit</scene>. 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 [https://en.wikipedia.org/wiki/Electron_acceptor electron acceptor] by [https://en.wikipedia.org/wiki/Catalysis catalyzing] the [https://en.wikipedia.org/wiki/Hydroquinone#Redox 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> [https://en.wikipedia.org/wiki/Electron_transfer transfers] the electrons to heme b595, which transfers them to the active site heme d<ref name= "Safarian">PMID:31604309</ref>. Multiple residues help stabilzie this electron trasnfer including a conserved <scene name='83/832931/Trp441/6'>Trp441</scene> that 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 also 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 the <scene name='83/832924/Cydb_subunit/2'>CydB subunit</scene> 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 <scene name='83/832924/Cyda_subunit/6'>CydA subunit</scene>. 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 [https://en.wikipedia.org/wiki/Electron_acceptor electron acceptor] by [https://en.wikipedia.org/wiki/Catalysis catalyzing] the [https://en.wikipedia.org/wiki/Hydroquinone#Redox 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> [https://en.wikipedia.org/wiki/Electron_transfer transfers] the electrons to heme b595, which transfers them to the active site heme d<ref name= "Safarian">PMID:31604309</ref>. Multiple residues help stabilzie this electron trasnfer including a conserved <scene name='83/832931/Trp441/6'>Trp441</scene> that 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 also 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 the <scene name='83/832924/Cydb_subunit/2'>CydB subunit</scene> mimics the triangular formation to stabilize the subunit<ref name="Safarian">PMID:31604309</ref>. | ||
===Mechanism=== | ===Mechanism=== | ||
A reduced quinol with two electrons received from NADH, pyruvate, D-lactate, or acyl coenzyme A transfers these electrons to heme b<sub>558</sub> and releases two protons into the periplasmic space as the initial [https://en.wikipedia.org/wiki/Electron_donor electron donor]. <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/2'>H-channel</scene> collects protons and the <scene name='83/832931/O_channel_overall/3'>O-channel</scene> collects oxygen atoms from the cytoplasmic side. The protons and oxygen flow to the active site heme d (Fig. 3). With electrons, oxygen, and protons available, heme d can successfully reduce dioxygen to water (Fig. 2, 4). Using oxygen as the final electron acceptor generates an exergonic reaction that can be coupled with the movement of protons against their gradient when quinol releases two protons into the periplasmic space and when the H-channel uptakes protons from the cytoplasmic side and transfers them to heme d<ref name="Safarian">PMID: 31604309</ref><ref name="Alexander">PMID:31723136</ref>. [[Image:mech4.png|500 px|center|thumb|''Figure 4''. General mechanism of cytochrome bd-oxidase in ''E. coli''. Electrons are passed from quinol to heme b<sub>558</sub> to heme b<sub>595</sub> to heme d. Protons and oxygen atoms flow into the H-channel and O-channel to heme d. Heme d catalyzes the reduction of oxygen to water.]] | |||
== Relevance == | == Relevance == | ||
The cytochrome ''bd'' oxidase is essential for [https://en.wikipedia.org/wiki/Pathogenic_bacteria pathogenic bacteria] to thrive in the human body because it enhances bacterial growth and [https://en.wikipedia.org/wiki/Bacterial_growth colonization]. Any alteration of the ''bd'' oxidase Cyd subunits will most likely produce a nonfunctional [https://en.wikipedia.org/wiki/Mutant mutant] cytochrome ''bd'' oxidase<ref name="Moosa">PMID: 28760899</ref>, which inhibits bacterial growth. If ''E. coli'' are missing or possess ineffective CydA and B subunits, bacterial growth ceases.<ref name="Hughes">PMID: 28182951</ref>. With [https://en.wikipedia.org/wiki/Colitis colitis], ''E. coli'' mutants that were missing CydAB colonized poorly in comparison to the [https://en.wikipedia.org/wiki/Wild_type wild type] levels of colonization<ref name="Hughes">PMID: 28182951</ref>. The cytochrome ''bd'' oxidase is the main component in [https://en.wikipedia.org/wiki/Biological_functions_of_nitric_oxide#Effects_in_bacteria nitric oxide] (NO) tolerance in bacteria, which is released by [https://en.wikipedia.org/wiki/Neutrophil neutrophils] and [https://en.wikipedia.org/wiki/Macrophage macrophages] when the [https://en.wikipedia.org/wiki/Host_(biology) host] is infected<ref name="Shepherd">PMID: 27767067</ref>. ''E. coli'' growth seen in [https://en.wikipedia.org/wiki/Urinary_tract_infection urinary tract infections] is mainly due to the NO resistant ''bd'' oxidase. Without the CydA and CydB subunits, bacteria could not colonize in high NO conditions<ref name="Shepherd">PMID: 27767067</ref>. Cytochrome ''bd'' oxidases are essential for life in other pathogenic bacteria such as [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''M. tuberculosis'']. Deletion of the CydA and CydB subunits dramatically decreased the growth of ''M. tb'' compared to the wild type when exposed to [https://en.wikipedia.org/wiki/Imidazopyridine imidazo[1,2-]][https://en.wikipedia.org/wiki/Imidazopyridine pyridine], a known [https://en.wikipedia.org/wiki/Enzyme_inhibitor inhibitor] of respiratory enzymes<ref name="Arora">PMID:25155596</ref>. [https://en.wikipedia.org/wiki/Downregulation_and_upregulation Upregulation] of the cytochrome ''bd'' oxidase Cyd genes resulted in a mutant strain of ''M. tb'' that was [https://en.wikipedia.org/wiki/Antimicrobial_resistance resistant] to imidazo[1,2-α]pyridine<ref name="Arora">PMID:25155596</ref>. | The cytochrome ''bd'' oxidase is essential for [https://en.wikipedia.org/wiki/Pathogenic_bacteria pathogenic bacteria] to thrive in the human body because it enhances bacterial growth and [https://en.wikipedia.org/wiki/Bacterial_growth colonization]. Any alteration of the ''bd'' oxidase Cyd subunits will most likely produce a nonfunctional [https://en.wikipedia.org/wiki/Mutant mutant] cytochrome ''bd'' oxidase<ref name="Moosa">PMID: 28760899</ref>, which inhibits bacterial growth. If ''E. coli'' are missing or possess ineffective CydA and B subunits, bacterial growth ceases.<ref name="Hughes">PMID: 28182951</ref>. With [https://en.wikipedia.org/wiki/Colitis colitis], ''E. coli'' mutants that were missing CydAB colonized poorly in comparison to the [https://en.wikipedia.org/wiki/Wild_type wild type] levels of colonization<ref name="Hughes">PMID: 28182951</ref>. The cytochrome ''bd'' oxidase is the main component in [https://en.wikipedia.org/wiki/Biological_functions_of_nitric_oxide#Effects_in_bacteria nitric oxide] (NO) tolerance in bacteria, which is released by [https://en.wikipedia.org/wiki/Neutrophil neutrophils] and [https://en.wikipedia.org/wiki/Macrophage macrophages] when the [https://en.wikipedia.org/wiki/Host_(biology) host] is infected<ref name="Shepherd">PMID: 27767067</ref>. ''E. coli'' growth seen in [https://en.wikipedia.org/wiki/Urinary_tract_infection urinary tract infections] is mainly due to the NO resistant ''bd'' oxidase. Without the CydA and CydB subunits, bacteria could not colonize in high NO conditions<ref name="Shepherd">PMID: 27767067</ref>. Cytochrome ''bd'' oxidases are essential for life in other pathogenic bacteria such as [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''M. tuberculosis'']. Deletion of the CydA and CydB subunits dramatically decreased the growth of ''M. tb'' compared to the wild type when exposed to [https://en.wikipedia.org/wiki/Imidazopyridine imidazo[1,2-]][https://en.wikipedia.org/wiki/Imidazopyridine pyridine], a known [https://en.wikipedia.org/wiki/Enzyme_inhibitor inhibitor] of respiratory enzymes<ref name="Arora">PMID:25155596</ref>. [https://en.wikipedia.org/wiki/Downregulation_and_upregulation Upregulation] of the cytochrome ''bd'' oxidase Cyd genes resulted in a mutant strain of ''M. tb'' that was [https://en.wikipedia.org/wiki/Antimicrobial_resistance resistant] to imidazo[1,2-α]pyridine<ref name="Arora">PMID:25155596</ref>. | ||