3ABM

Bovine heart cytochrome c oxidase at the fully oxidized state (200-s X-ray exposure dataset)

Summary for 3ABM

• Entry DOI: 10.2210/pdb3abm/pdb
• Related: 1OCC 1OCO 1OCR 1OCZ 1V54 1V55 2DYR 2DYS 2EIJ 2EIK 2EIL 2EIM 2EIN 2OCC 2ZXW 3ABL
• Descriptor: Cytochrome c oxidase subunit 1, Cytochrome c oxidase polypeptide 7A1, Cytochrome c oxidase subunit 7B, ... (29 entities in total)
• Functional Keywords: oxidoreductase, copper, electron transport, formylation, heme, iron, membrane, mitochondrion, mitochondrion inner membrane, respiratory chain, transmembrane, transport, acetylation, transit peptide, zinc, isopeptide bond, ubl conjugation
• Biological source: Bos taurus (bovine); More
• Cellular location: Mitochondrion inner membrane; Multi-pass membrane protein: P00396 P68530 P00415; Mitochondrion inner membrane: P07470 P13183 P00430 P10175 P00423 P00426 P00428 P07471 P04038; Mitochondrion intermembrane space: P00429
• Total number of polymer chains: 26
• Total formula weight: 442820.00

Authors

Aoyama, H.,Muramoto, K.,Shinzawa-Itoh, K.,Yamashita, E.,Tsukihara, T.,Ogura, T.,Yoshikawa, S. (deposition date: 2009-12-16, release date: 2010-01-19, Last modification date: 2023-11-01)

Primary citation

Aoyama, H.,Muramoto, K.,Shinzawa-Itoh, K.,Hirata, K.,Yamashita, E.,Tsukihara, T.,Ogura, T.,Yoshikawa, S.
A peroxide bridge between Fe and Cu ions in the O2 reduction site of fully oxidized cytochrome c oxidase could suppress the proton pump
Proc.Natl.Acad.Sci.USA, 106:2165-2169, 2009

PubMed Abstract: The fully oxidized form of cytochrome c oxidase, immediately after complete oxidation of the fully reduced form, pumps protons upon each of the initial 2 single-electron reduction steps, whereas protons are not pumped during single-electron reduction of the fully oxidized "as-isolated" form (the fully oxidized form without any reduction/oxidation treatment) [Bloch D, et al. (2004) The catalytic cycle of cytochrome c oxidase is not the sum of its two halves. Proc Natl Acad Sci USA 101:529-533]. For identification of structural differences causing the remarkable functional difference between these 2 distinct fully oxidized forms, the X-ray structure of the fully oxidized as-isolated bovine heart cytochrome c oxidase was determined at 1.95-A resolution by limiting the X-ray dose for each shot and by using many (approximately 400) single crystals. This minimizes the effects of hydrated electrons induced by the X-ray irradiation. The X-ray structure showed a peroxide group bridging the 2 metal sites in the O(2) reduction site (Fe(3+)-O(-)-O(-)-Cu(2+)), in contrast to a ferric hydroxide (Fe(3+)-OH(-)) in the fully oxidized form immediately after complete oxidation from the fully reduced form, as has been revealed by resonance Raman analyses. The peroxide-bridged structure is consistent with the reductive titration results showing that 6 electron equivalents are required for complete reduction of the fully oxidized as-isolated form. The structural difference between the 2 fully oxidized forms suggests that the bound peroxide in the O(2) reduction site suppresses the proton pumping function.

PubMed: 19164527
DOI: 10.1073/pnas.0806391106

Experimental method

X-RAY DIFFRACTION (1.95 Å)