Structure

The focus of this page is to explain the structure and function of the G. thermodenitrificans’ bd oxidase. The contains that are arranged in a nearly oval shape.^[2] The protein contains two structurally similar subunits, , seen in blue, and , seen in red, each containing nine helices, and one smaller subunit, , in teal, with one transmembrane helix. These subunits interact using hydrophobic residues and symmetry at the interfaces. The CydX subunit, whose function is not currently known, is positioned in the same way as CydS, a separate subunit that is found in the bd oxidase homologue from E. coli bd oxidase, but is not found in G. thermodenitrificans. Due to its similar structure and position to CydS, CydX has been hypothesized to potentially stabilize during potential structural rearrangements of the Q loop upon binding and oxidation of ubiquinone (Figure 1), the function of CydS in E. coli^[2] The is a hydrophilic region above Cyd A. The lack of hydrogen bonding in this hydrophobic protein allows the protein to be flexible and go through a large conformational change for reduction of dioxygen. is mostly involved in the proton pathway, and is involved with the oxygen pathway.

Other structures of bd oxidase exist that contain a variety of potential routes for the different reactants of the reduction of oxygen. For example, the bd oxidase of E. coli contains a different orientation of the Hemes and many different mechanisms of proton shuttling. G. thermodenitrificans was chosen because of the interest in the unique proton pathways, as described in the “Potential Proton Pathways” section.

Active Site

Figure 1. The active site of bd oxidase for G. thermodenitrificans. Heme B558 (pink; left), Heme B595 (pink; right), and Heme D (green). Important residues shown in blue. Measurements are shown in Å.

The active site for bd oxidase in G. thermodenitrificans is located in subunit Cyd A. The site consists of three iron hemes: , , and that are held together in a rigid triangular due to Van der Waals interactions.^[2] The between each heme's central iron is relatively constant which serves to shuttle protons and electrons from one heme to another efficiently (Figure 1). is hypothesized to act as an electron acceptor, orientated toward the extracellular side by (Figure 1).^[2] With closest in proximity to the intracellular side, Heme B559 is likely the proton acceptor with two potential proton pathways. Both and then shuttle their respective ions directly to as this is the shortest pathway.

Potential Oxygen Entry Site

is the hypothesized spot for the to enter the protein. Heme D (shown in green) is directly connected to the protein surface on CydA and contains a solvent accessible substrate channel. This channel and accessibility allow for oxygen to easily bind to Heme D and eventually be reduced to two H₂O molecules. This process requires a proton and electron source, both described in the later sections.

Electron Source

Figure 2. Chemical structure of ubiquinone.

Potential Proton Pathways

Figure 3. Two potential sources of protons: CydA and CydB pathway.

Because there is no proton pump present, the proton transfer mechanism is facilitated by via intracellular water molecules.

One potential proton pathway is formed from the of . It is called the . The residues along this pathway help facilitate the movement of the protons. The location and negative charge characteristic of , together with previous mutagenesis experiments, supports the proposal that this glutamate residue is a redox state-dependent mediator of proton transfer to a charge compensation site. In other words, it acts like a proton shuttle.^[2] The , which is the last residue in this pathway, could be the protonatable group eventually used upon reduction. More research needs to be done to determine whether the CydA pathway is solely providing protons for charge compensation, or whether can be a branching point that is able to pass protons via the propionates to the oxygen-binding site.^[4]

Another potential entry site is close to the of and is referred to as the . In this pathway, is thought to be the equivalent of the in the CydA pathway.^[2] The other residues help facilitate the movement of the proton very similarly to the . The is the most accepted source of protons as less is known about the .

Overall Oxygen Reduction Mechanism Summary

Figure 4. Overall oxidation-reduction mechanism summary.

As mentioned above, the purpose of the bd oxidase is to reduce O₂ to 2H₂O using quinol as the reducing substrate, yielding the overall reaction of O₂ + 4H⁺ + 4e^- → 2H₂O. The oxygen comes from the extracellular side of the protein, and enters through the to . This pathway is depicted in orange in Figure 4.

The electrons required for the reduction mechanism come from a ubiquinol molecule (Figure 2) that simultaneously binds to the and gets oxidized giving 4e^- to . Once at , the 4e^- will be shuttled directly to to be used in the reaction. The electron pathway is depicted in blue in Figure 4.

The protons that are required in the pathway are not provided by a pump, but rather via intracellular water. The utilize amino acids with properties that help shuttle the protons from the intracellular side of the protein to in the active site. The passes through the , shown in purple in Figure 4. The proceeds through the , shown in green in Figure 4.

When all of these elements of the reduction reaction aggregate in the active site at their respective hemes, the protons and electrons are shuttled to , where the actual reduction occurs. The 2H₂O molecules are then expelled from , shown in red in Figure 4. The shuttling of these electrons and protons also helps assist with creating the electric chemical potential in the cellular membrane.

Structure Similarity to bd oxidase found in E. coli

Figure 5. Alignment of bd oxidase for the organisms G. thermodenitrificans (PDB: 5doq) shown in blue and E. coli (PDB: 6rko) shown in purple.

Figure 6. Heme arrangements for the organisms G. thermodenitrificans and E. coli. Heme D shown in green; Heme B595 and Heme B558 shown in pink