Sandbox Reserved 1625: Difference between revisions

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OCA, Emily Neal, Grace A. Bassler, Marisa Villarreal

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 [[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 previously mentioned 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 6RX4'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.
+[[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 6RX4'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==
 === Subunits ===