2Y69

Bovine heart cytochrome c oxidase re-refined with molecular oxygen

Summary for 2Y69

• Entry DOI: 10.2210/pdb2y69/pdb
• Related: 1OCC 1OCO 1OCR 1OCZ 1V54 1V55 2OCC
• Descriptor: CYTOCHROME C OXIDASE SUBUNIT 1, CYTOCHROME C OXIDASE POLYPEPTIDE 7A1, CYTOCHROME C OXIDASE POLYPEPTIDE 7B, ... (24 entities in total)
• Functional Keywords: electron transport, complex iv, proton pumps, membrane protein
• Biological source: BOS TAURUS (CATTLE); More
• Total number of polymer chains: 26
• Total formula weight: 464224.97

Authors

Kaila, V.R.I.,Oksanen, E.,Goldman, A.,Verkhovsky, M.I.,Sundholm, D.,Wikstrom, M. (deposition date: 2011-01-20, release date: 2011-02-23, Last modification date: 2024-10-23)

Primary citation

Kaila, V.R.I.,Oksanen, E.,Goldman, A.,Bloch, D.A.,Verkhovsky, M.I.,Sundholm, D.,Wikstrom, M.
A Combined Quantum Chemical and Crystallographic Study on the Oxidized Binuclear Center of Cytochrome C Oxidase.
Biochim.Biophys.Acta, 1807:769-, 2011

PubMed Abstract: Cytochrome c oxidase (CcO) is the terminal enzyme of the respiratory chain. By reducing oxygen to water, it generates a proton gradient across the mitochondrial or bacterial membrane. Recently, two independent X-ray crystallographic studies ((Aoyama et al. Proc. Natl. Acad. Sci. USA 106 (2009) 2165-2169) and (Koepke et al. Biochim. Biophys. Acta 1787 (2009) 635-645)), suggested that a peroxide dianion might be bound to the active site of oxidized CcO. We have investigated this hypothesis by combining quantum chemical calculations with a re-refinement of the X-ray crystallographic data and optical spectroscopic measurements. Our data suggest that dianionic peroxide, superoxide, and dioxygen all form a similar superoxide species when inserted into a fully oxidized ferric/cupric binuclear site (BNC). We argue that stable peroxides are unlikely to be confined within the oxidized BNC since that would be expected to lead to bond splitting and formation of the catalytic P intermediate. Somewhat surprisingly, we find that binding of dioxygen to the oxidized binuclear site is weakly exergonic, and hence, the observed structure might have resulted from dioxygen itself or from superoxide generated from O(2) by the X-ray beam. We show that the presence of O(2) is consistent with the X-ray data. We also discuss how other structures, such as a mixture of the aqueous species (H(2)O+OH(-) and H(2)O) and chloride fit the experimental data.

PubMed: 21211513
DOI: 10.1016/J.BBABIO.2010.12.016

Experimental method

X-RAY DIFFRACTION (1.95 Å)