Sandbox Reserved 1605

This Sandbox is Reserved from Jan 13 through September 1, 2020 for use in the course CH462 Biochemistry II taught by R. Jeremy Johnson at the Butler University, Indianapolis, USA. This reservation includes Sandbox Reserved 1598 through Sandbox Reserved 1627.

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Cytochrome bd-1 oxidase in Escherichia coliCytochrome bd-1 oxidase in Escherichia coli

IntroductionIntroduction

<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.'

Function

The <scene name='83/832931/Full/4'>cytochrome bd oxidase</scene> allows bacteria to be resistant to hypoxia, cyanide, nitric oxide, and H₂O₂

Molecular FunctionMolecular Function

H and O channelsH and O channels

Figure 3. H and o-channels of cytochrome bd-oxidase in E. coli. Channels are outlined in gray, water is shown as spheres, and various amino acids are labeled above.

The hydrogen and oxygen channels (Fig. 3) are essential for H⁺ and O₂ molecules to reach the active site of cytochrome bd oxidase. A proton motive force generated by the oxidase allows protons from the cytoplasm to flow through a hydrophilic full of water (pink dots), entering at and moving past where they can be transferred to the active site with the help of the conserved residues . A smaller 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 in CydB and passing by , 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.

Interestingly, the o-channel does not exist in the cytochromebd oxidase of Geobacillus thermodenitrificans; instead, oxygen binds directly to the active site. The 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. thermodenitrificans bd oxidase contributes more to detoxification.

HemesHemes

Three are present in the CydA subunit. These three hemes form a triangle to maximize subunit stability, which is an evolutionary conserved feature across bd oxidases. Heme b₅₅₈ acts as the primary electron acceptor by catalyzing the oxidation of quinol. Conserved help to stabilize heme b558. Heme b₅₅₈ transfers the electrons to heme b595, which transfers them to the active site heme d. A conserved assists heme b₅₉₅ in transferring electrons to heme d. A conserved is essential for charge stabilization of heme b₅₉₅, while stabilizes heme d. As heme d collects the electrons from heme b₅₉₅, in the o-channel facilities the binding of oxygen to heme d, and in the h-channel facilitate proton transfer to heme d. Similar to the three hemes, the (UQ-8) molecule found in CydB mimics the triangular formation to stabilize the subunit.

MechanismMechanism

Quinol is used as the initial electron donor and heme b₅₅₈ is the initial electron acceptor. transfers the electrons to , which transfers the electrons to . Concurrently, the will collect hydrogen atoms and will collect oxygen atoms that will flow to heme d (Fig. 3). With electrons, oxygen, and protons available, heme d can successfully reduce dioxygen to water (Fig. 4).

RelevanceRelevance

The cytochrome bd oxidase is essential for bacteria to thrive in the human body. Any alteration of the bacterial Cyd subunits produces a nonfunctional mutant cytochrome bd oxidase, which inhibits bacterial growth. Bacterial terminal oxidases are essential for formate oxidation activity, which enhances bacterial growth. If E. coli were missing or possessed ineffective CydA and B subunits, their growth advantage was eliminated. With colitis, E. coli mutants that were missing CydAB colonized poorly, in comparison to the wild type levels of colonization. The cytochrome bd oxidase is the main component in nitric oxide (NO) tolerance in bacteria, which is released by neutrophils and macrophages when the host is infected. E. coli growth seen in urinary tract infections is mainly due to the NO resistant bd oxidase. Without the CydA and CydB subunits, bacteria could not colonize in high NO conditions. Cytochrome bd oxidases are essential in other pathogenic bacteria such as M. tuberculosis. Deletion of the CydA and CydB subunits dramatically decreased the growth of M. tb when exposed to imidazo[1,2-α]pyridine, a known inhibitor of ATP synthase.

Since cytochrome bd oxidases are only found in prokaryotes and are required for pathogenic bacterial infections, inhibitors that target cytochrome bd oxidase are promising antibacterial agents. Compounds that target heme b₅₅₈, create unusable forms of oxygen, and target the o-channel have shown potential in halting bacterial growth.