9IKH

Bovine Heart Cytochrome c Oxidase in the Nitrous Oxide-bound Fully Oxidized State

Summary for 9IKH

• Entry DOI: 10.2210/pdb9ikh/pdb
• Related: 9IKF 9IKG 9IKI
• Descriptor: Cytochrome c oxidase subunit 1, Cytochrome c oxidase subunit 7A1, Cytochrome c oxidase subunit 7B, mitochondrial, ... (30 entities in total)
• Functional Keywords: nitrous oxide, fully oxidized, oxidoreductase
• Biological source: Bos taurus (cattle); More
• Total number of polymer chains: 26
• Total formula weight: 459323.22

Authors

Muramoto, K.,Ide, T.,Shinzawa-Itoh, K. (deposition date: 2024-06-27, release date: 2025-07-02, Last modification date: 2025-07-23)

Primary citation

Muramoto, K.,Ide, T.,Shinzawa-Itoh, K.
The binding sites of carbon dioxide, nitrous oxide, and xenon reveal a putative exhaust channel for bovine cytochrome c oxidase.
J.Biol.Chem., 301:110395-110395, 2025

PubMed Abstract: Cytochrome c oxidase (CcO) catalyzes oxygen (O) reduction at the heme a-Cu 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 a-Cu site is the O transfer pathway. Gas molecules other than O, including carbon dioxide (CO) generated in the TCA 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 CO-, nitrous oxide (NO)-, and Xe-bound bovine CcO in the oxidized and reduced states at resolutions of 1.75-1.85 Å. Binding of Xe in the channel of subunit I near the interface with subunit III supported the proposed O transfer pathway. CO, NO, and another Xe were all bound to a common site near the branching point of another hydrophobic channel that branched from the O 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, CO that has entered the O pathway could be passively expelled through this channel. This channel consists of subunits 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 CO exhaust pathway.

PubMed: 40543594
DOI: 10.1016/j.jbc.2025.110395

Experimental method

X-RAY DIFFRACTION (1.75 Å)