7YPY

Bovine heart cytochrome c oxidase in fully oxidized state at 1.5 angstrom resolution

Summary for 7YPY

• Entry DOI: 10.2210/pdb7ypy/pdb
• Descriptor: Cytochrome c oxidase subunit 1, Cytochrome c oxidase subunit 7A1, mitochondrial, Cytochrome c oxidase subunit 7B, mitochondrial, ... (31 entities in total)
• Functional Keywords: respiratory enzyme, membrane protein, hemeprotein, protein complex, oxidoreductase
• Biological source: Bos taurus (Bovine); More
• Total number of polymer chains: 26
• Total formula weight: 460223.76

Authors

Shimada, A.,Tsukihara, T. (deposition date: 2022-08-05, release date: 2022-09-21, Last modification date: 2023-11-29)

Primary citation

Yano, N.,Muramoto, K.,Shimada, A.,Shinzawa-Itoh, K.,Tsukihara, T.,Yoshikawa, S.
The Mg2+-containing water cluster of mammalian cytochrome c oxidase collects four pumping proton equivalents in each catalytic cycle.
J. Biol. Chem., 291:23882-23894, 2016

PubMed Abstract: Bovine heart cytochrome c oxidase (CcO) pumps four proton equivalents per catalytic cycle through the H-pathway, a proton-conducting pathway, which includes a hydrogen bond network and a water channel operating in tandem. Protons are transferred by HO through the water channel from the N-side into the hydrogen bond network, where they are pumped to the P-side by electrostatic repulsion between protons and net positive charges created at heme a as a result of electron donation to O bound to heme a To block backward proton movement, the water channel remains closed after O binding until the sequential four-proton pumping process is complete. Thus, the hydrogen bond network must collect four proton equivalents before O binding. However, a region with the capacity to accept four proton equivalents was not discernable in the x-ray structures of the hydrogen bond network. The present x-ray structures of oxidized/reduced bovine CcO are improved from 1.8/1.9 to 1.5/1.6 Å resolution, increasing the structural information by 1.7/1.6 times and revealing that a large water cluster, which includes a Mg ion, is linked to the H-pathway. The cluster contains enough proton acceptor groups to retain four proton equivalents. The redox-coupled x-ray structural changes in Glu, which bridges the Mg and Cu (the initial electron acceptor from cytochrome c) sites, suggest that the Cu-Glu-Mg system drives redox-coupled transfer of protons pooled in the water cluster to the H-pathway. Thus, these x-ray structures indicate that the Mg-containing water cluster is the crucial structural element providing the effective proton pumping in bovine CcO.

PubMed: 27605664
DOI: 10.1074/JBC.M115.711770

Experimental method

X-RAY DIFFRACTION (1.5 Å)