Sandbox Reserved 1625: Difference between revisions
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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| | [[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]. | ||
