Sandbox Reserved 1616
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| - | ==bd Oxidase, | + | ==bd Oxidase, 6RX4== |
<StructureSection load='6rx4' size='350' frame='true' side='right' caption='E. coli cytochrome bd-1 oxidase' scene='83/832931/Full/3'> | <StructureSection load='6rx4' size='350' frame='true' side='right' caption='E. coli cytochrome bd-1 oxidase' scene='83/832931/Full/3'> | ||
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bd Oxidase is a type of quinol-dependent terminal oxidase found exclusively in prokaryotes. 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. | bd Oxidase is a type of quinol-dependent terminal oxidase found exclusively in prokaryotes. 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 | + | [[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.]] |
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| - | The overall mechanism of bd oxidases involves an exergonic reduction reaction of molecular oxygen into water. 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. | + | 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. |
| - | [[Image: 5doq_WHOLE_IMAGE.png|300 px|left|thumb|Figure 2: 6RX4 monomer subunit; alpha helices in teal, beta sheets in purple.]] | ||
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| - | 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 four protein subunits will be of primary focus when identifying the relationship between structure and function. | + | 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_6rx4/3'>four protein subunits</scene> will be of primary focus when identifying the relationship between structure and function. |
== Function == | == Function == | ||
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== Structural highlights == | == Structural highlights == | ||
| - | [[Image:Q Loop.png|400 px|right|thumb|Figure 1]] | ||
Current revision
bd Oxidase, 6RX4
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![Figure 1: Overall schematic representation of cytochrome bd [1]; 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. Hemeb558 is involved in quinol oxidation and Hemed serves as the site where O2 binds and becomes reduced to H2O.](/wiki/index.php/Image:Proton_graadient.jpg)
References
- ↑ 1.0 1.1 Safarian S, Rajendran C, Muller H, Preu J, Langer JD, Ovchinnikov S, Hirose T, Kusumoto T, Sakamoto J, Michel H. Structure of a bd oxidase indicates similar mechanisms for membrane-integrated oxygen reductases. Science. 2016 Apr 29;352(6285):583-6. doi: 10.1126/science.aaf2477. PMID:27126043 doi:http://dx.doi.org/10.1126/science.aaf2477
- ↑ 2.0 2.1 Ransey E, Paredes E, Dey SK, Das SR, Heroux A, Macbeth MR. Crystal structure of the Entamoeba histolytica RNA lariat debranching enzyme EhDbr1 reveals a catalytic Zn(2+) /Mn(2+) heterobinucleation. FEBS Lett. 2017 Jul;591(13):2003-2010. doi: 10.1002/1873-3468.12677. Epub 2017, Jun 14. PMID:28504306 doi:http://dx.doi.org/10.1002/1873-3468.12677
