The binding sites of carbon dioxide, nitrous oxide, and xenon reveal a putative exhaust channel for bovine cytochrome c oxidase

Cytochrome c oxidase (CcO) catalyzes oxygen (O₂) reduction at the heme a₃-Cu_B site in the transmembrane region of the enzyme. It has been proposed that the hydrophobic channel that connects the transmembrane surface of subunit III through subunit I to the heme a₃-Cu_B site is the O₂ transfer pathway. Gas molecules other than O₂, including carbon dioxide (CO₂) generated in the tricarboxylic acid cycle, should also enter the hydrophobic channel, but it is not clear how these molecules are expelled from CcO. We analyzed the crystal structures of CO₂-, nitrous oxide-, and Xe-bound bovine CcO in the oxidized and reduced states at resolutions of 1.75 to 1.85 Å. Binding of Xe in the channel of subunit I near the interface with subunit III supported the proposed O₂ transfer pathway. CO₂, nitrous oxide, and another Xe were all bound to a common site near the branching point of another hydrophobic channel that branched from the O₂ transport channel. Additional Xe atoms were bound in the second channel leading up to the molecular surface on the intermembrane space side, suggesting that under physiological conditions, CO₂ that has entered the O₂ pathway could be passively expelled through this channel. This channel consists of subunit I and nuclear DNA-coded subunit VIIc, suggesting that the addition of subunit VIIc in the process of molecular evolution of mitochondrial CcO has made the CO₂ exhaust pathway.