7D5W

Bovine heart cytochrome c oxidase in a catalytic intermediate of O at 1.84 angstrom resolution

Summary for 7D5W

• Entry DOI: 10.2210/pdb7d5w/pdb
• Descriptor: Cytochrome c oxidase subunit 1, Cytochrome c oxidase subunit 7A1, mitochondrial, Cytochrome c oxidase subunit 7B, mitochondrial, ... (30 entities in total)
• Functional Keywords: cytochrome c oxidase membrane protein heme protein, oxidoreductase
• Biological source: Bos taurus (Bovine); More
• Total number of polymer chains: 26
• Total formula weight: 450206.60

Authors

Tsukihara, T.,Shimada, A. (deposition date: 2020-09-28, release date: 2021-07-21, Last modification date: 2023-11-29)

Primary citation

Shimada, A.,Hara, F.,Shinzawa-Itoh, K.,Kanehisa, N.,Yamashita, E.,Muramoto, K.,Tsukihara, T.,Yoshikawa, S.
Critical roles of the Cu B site in efficient proton pumping as revealed by crystal structures of mammalian cytochrome c oxidase catalytic intermediates.
J.Biol.Chem., 297:100967-100967, 2021

PubMed Abstract: Mammalian cytochrome c oxidase (CcO) reduces O to water in a bimetallic site including Fe and Cu giving intermediate molecules, termed A-, P-, F-, O-, E-, and R-forms. From the P-form on, each reaction step is driven by single-electron donations from cytochrome c coupled with the pumping of a single proton through the H-pathway, a proton-conducting pathway composed of a hydrogen-bond network and a water channel. The proton-gradient formed is utilized for ATP production by F-ATPase. For elucidation of the proton pumping mechanism, crystal structural determination of these intermediate forms is necessary. Here we report X-ray crystallographic analysis at ∼1.8 Å resolution of fully reduced CcO crystals treated with O for three different time periods. Our disentanglement of intermediate forms from crystals that were composed of multiple forms determined that these three crystallographic data sets contained ∼45% of the O-form structure, ∼45% of the E-form structure, and ∼20% of an oxymyoglobin-type structure consistent with the A-form, respectively. The O- and E-forms exhibit an unusually long Cu-OH distance and Cu-HO structure keeping Fe-OH state, respectively, suggesting that the O- and E-forms have high electron affinities that cause the O→E and E→R transitions to be essentially irreversible and thus enable tightly coupled proton pumping. The water channel of the H-pathway is closed in the O- and E-forms and partially open in the R-form. These structures, together with those of the recently reported P- and F-forms, indicate that closure of the H-pathway water channel avoids back-leaking of protons for facilitating the effective proton pumping.

PubMed: 34274318
DOI: 10.1016/j.jbc.2021.100967

Experimental method

X-RAY DIFFRACTION (1.84 Å)