Sandbox Reserved 1625: Difference between revisions

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==Introduction==

~~transmembrane (Fig. 2)~~ [[Image:Transmem1.png|300 px|right|thumb|'''Figure 2''. Cartoon model of cytochrome bd-oxidase in ''E. coli''. Dashed lines represent borders of cytoplasmic and extracellular regions.]]

[[Image:Transmem1.png|300 px|right|thumb|'''Figure 2''. Cartoon model of cytochrome bd-oxidase in ''E. coli''. Dashed lines represent borders of cytoplasmic and extracellular regions.]]

bd Oxidase is a type of quinol-dependent terminal oxidase found exclusively in prokaryotes.<ref name="Safarian">PMID: 27126043</ref> With a very high oxygen affinity, bd oxidases play a vital role in the oxidative phosphorylation pathway in both gram-positive and gram-negative bacteria. bd oxidases responsibility in the oxidative phosphorylation pathway allows the protein to also assist as a key survival factor in the bacterial stress response against antibacterial drugs. 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.

[[Image:proton graadient.jpg|300 px|left|thumb|Figure 1: Overall schematic representation of cytochrome bd [https://doi.org/10.1016/j.bbabio.2014.01.016.]; 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''b558'' is involved in quinol oxidation and Heme''d'' serves as the site where O2 binds and becomes reduced to H2O.]]

The overall mechanism of bd oxidases involves an exergonic reduction reaction of molecular oxygen into water (Figure 1). During this reaction, a proton gradient is generated in order to assist in the conservation of energy. 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.

This page will be specifically focusing on the structure and overall function of the 6RX4 bd oxidase. 6RX4 is a part of the long(L) quinol-binding domain subfamily that terminal oxidases are classified into. The L-subfamily of bd oxidases are responsible for the survival of acute infectious diseases such as E.Coli and 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_6rx4/2'>four protein subunits</scene> will be of primary focus when identifying the relationship between structure and function.

The <scene name='83/832931/Full/4'>cytochrome ''bd'' oxidase</scene> allows bacteria to be resistant to hypoxia, cyanide, nitric oxide, and H<sub>2</sub>O<sub>2</sub><ref name="Harikishore">PMID: 31939065</ref>

==Structure==

=== Subunits ===

Sandbox Reserved 1625: Difference between revisions

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 <StructureSection  load='6rx4'  size='350'  frame='true' side='right' caption='E. coli cytochrome bd-1 oxidase. Blue= CydA; green= CydB; yellow= CydX; pink= CydS; gray = hemes and UQ-8.' scene='83/832931/Full/3'>
 ==Introduction==
-transmembrane (Fig. 2) [[Image:Transmem1.png|300 px|right|thumb|'''Figure 2''. Cartoon model of cytochrome bd-oxidase in ''E. coli''. Dashed lines represent borders of cytoplasmic and extracellular regions.]]
+[[Image:Transmem1.png|300 px|right|thumb|'''Figure 2''. Cartoon model of cytochrome bd-oxidase in ''E. coli''. Dashed lines represent borders of cytoplasmic and extracellular regions.]]
+bd Oxidase is a type of quinol-dependent terminal oxidase found exclusively in prokaryotes.<ref name="Safarian">PMID: 27126043</ref>  With a very high oxygen affinity, bd oxidases play a vital role in the oxidative phosphorylation pathway in both gram-positive and gram-negative bacteria. bd oxidases responsibility in the oxidative phosphorylation pathway allows the protein to also assist as a key survival factor in the bacterial stress response against antibacterial drugs. 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.
+[[Image:proton graadient.jpg|300 px|left|thumb|Figure 1: Overall schematic representation of cytochrome bd [https://doi.org/10.1016/j.bbabio.2014.01.016.]; 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''b558'' is involved in quinol oxidation and Heme''d'' serves as the site where O2 binds and becomes reduced to H2O.]]
+The overall mechanism of bd oxidases involves an exergonic reduction reaction of molecular oxygen into water (Figure 1). During this reaction, a proton gradient is generated in order to assist in the conservation of energy. 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.
+This page will be specifically focusing on the structure and overall function of the 6RX4 bd oxidase. 6RX4 is a part of the long(L) quinol-binding domain subfamily that terminal oxidases are classified into. The L-subfamily of bd oxidases are responsible for the survival of acute infectious diseases such as E.Coli and 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_6rx4/2'>four protein subunits</scene> will be of primary focus when identifying the relationship between structure and function.
 The <scene name='83/832931/Full/4'>cytochrome ''bd'' oxidase</scene> allows bacteria to be resistant to hypoxia, cyanide, nitric oxide, and H<sub>2</sub>O<sub>2</sub><ref name="Harikishore">PMID: 31939065</ref>
 ==Structure==
 === Subunits ===