test</scene’>

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Structural highlights

H and O channels

Figure 3

The hydrogen and oxygen channels (Fig. 3) are essential for H⁺ and O₂ molecules to reach the active site of bd oxidase. A proton motive force generated by the oxidase^[1] allows protons from the cytoplasm flow through a water-filled hydrophilic H-channel entering at D119^A and moving past Lys57^A, Lys109^B, Asp105^B, Tyr379^B, and Asp58^{B [2]} where they can be transferred to the active site with the help of the conserved residues Ser108^A, Glu107^A, and Ser140^A. A smaller o-channel 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 W63 in CydB and passing by Leu101^B, Ile114^A, and Glu99^A, which assists with the binding of oxygen to the active site. The o-channel channel is approximately 1.5 Å in diameter, which may help with selectivity. Inhbitors that target the o-channel by blocking its entrance are quite effective by preventing the reduction of oxygen to water.

Interestingly, the o-channel does not exist in the bd oxidase of Geobacillus thermodenitrificans; instead, oxygen binds directly to the active site. The CydS subunit found in E. coli blocks this alternate oxygen entry site, which allows oxygen to travel through the o-channel. The presence of an o-channel affects oxidase activity, as the E. coli oxidase acts as a "true" oxidase, while the G. th oxidase contributes more to detoxification.

Hemes

There are three molecules present in the CydA subunit that form a triangle to maximize subunit stability, which is an evolutionary conserved feature across bd oxidases. Similar to the hemes, the ubiquinone-8 (UQ-8) molecule found in CydB mimics the triangular formation to stabilize the subunit(safarian). Heme b₅₅₈ acts as the primary electron acceptor by catalyzing the oxidation of quinol. Conserved His186 and Met393 help to stabilize heme b558. Heme b₅₅₈ transfers the electrons from quinol to heme b595, which transfers them to the active site heme d. A conserved Trp441^A assists heme b₅₉₅ in transferring electrons to heme d. A conserved Glu445 is essential for charge stabilization of heme b₅₉₅, while His19 stabilizes heme d. As heme d collects the electrons from heme b₅₉₅, Glu99 in the o-channel facilities the binding of oxygen to heme d, and Ser108, Glu107, and Ser140 in the h-channel facilitate proton transfer to heme d. With electrons, oxygen, and protons available, heme d can successfully reduce dioxygen to water.

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