5Z84

The structure of azide-bound cytochrome c oxidase determined using the crystals exposed to 20 mM azide solution for 4 days

Summary for 5Z84

• Entry DOI: 10.2210/pdb5z84/pdb
• Related: 5Z85 5Z86
• Descriptor: Cytochrome c oxidase subunit 1, Cytochrome c oxidase subunit 7A1, mitochondrial, cytochrome c oxidase subunit 11, Cytochrome c oxidase subunit 7B, mitochondrial, ... (30 entities in total)
• Functional Keywords: metalloenzyme cytochrome c oxidase proton pump bioenergetics heme copper, oxidoreductase
• Biological source: Bos taurus (Bovine); More
• Total number of polymer chains: 26
• Total formula weight: 450116.12

Authors

Shimada, A.,Hatano, K.,Tadehara, H.,Tsukihara, T. (deposition date: 2018-01-31, release date: 2018-08-15, Last modification date: 2023-11-22)

Primary citation

Shimada, A.,Hatano, K.,Tadehara, H.,Yano, N.,Shinzawa-Itoh, K.,Yamashita, E.,Muramoto, K.,Tsukihara, T.,Yoshikawa, S.
X-ray structural analyses of azide-bound cytochromecoxidases reveal that the H-pathway is critically important for the proton-pumping activity.
J. Biol. Chem., 293:14868-14879, 2018

PubMed Abstract: Cytochrome oxidase (CcO) is the terminal oxidase of cellular respiration, reducing O to water and pumping protons. X-ray structural features have suggested that CcO pumps protons via a mechanism involving electrostatic repulsions between pumping protons in the hydrogen-bond network of a proton-conducting pathway (the H-pathway) and net positive charges created upon oxidation of an iron site, heme (Fe ), for reduction of O at another iron site, heme (Fe ). The protons for pumping are transferred to the hydrogen-bond network from the N-side via the water channel of the H-pathway. Back-leakage of protons to the N-side is thought to be blocked by closure of the water channel. To experimentally test this, we examined X-ray structures of the azide-bound, oxidized bovine CcO and found that an azide derivative (N-Fe , Cu-N) induces a translational movement of the heme plane. This was accompanied by opening of the water channel, revealing that Fe and the H-pathway are tightly coupled. The channel opening in the oxidized state is likely to induce back-leakage of pumping protons, which lowers the proton level in the hydrogen-bond network during enzymatic turnover. The proton level decrease weakens the electron affinity of Fe , if Fe electrostatically interacts with protons in the hydrogen-bond network. The previously reported azide-induced redox-potential decrease in Fe supports existence of the electrostatic interaction. In summary, our results indicate that the H-pathway is critical for CcO's proton-pumping function.

PubMed: 30077971
DOI: 10.1074/jbc.RA118.003123

Experimental method

X-RAY DIFFRACTION (1.85 Å)