5B1A

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

Summary for 5B1A

• Entry DOI: 10.2210/pdb5b1a/pdb
• Related: 5B1B
• Descriptor: Cytochrome c oxidase subunit 1, Cytochrome c oxidase subunit 7A1, mitochondrial, Cytochrome c oxidase subunit 7B, mitochondrial, ... (29 entities in total)
• Functional Keywords: oxidoreductase, proton pump, heme, respiratory chain
• Biological source: Bos taurus (Bovine); More
• Total number of polymer chains: 26
• Total formula weight: 442820.00

Authors

Yano, N.,Muramoto, K.,Shimada, A.,Takemura, S.,Baba, J.,Fujisawa, H.,Mochizuki, M.,Shinzawa-Itoh, K.,Yamashita, E.,Tsukihara, T.,Yoshikawa, S. (deposition date: 2015-12-01, release date: 2016-09-14, Last modification date: 2020-02-26)

Primary citation

Yano, N.,Muramoto, K.,Shimada, A.,Takemura, S.,Baba, J.,Fujisawa, H.,Mochizuki, M.,Shinzawa-Itoh, K.,Yamashita, E.,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)