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Respiratory Conservation of Energy with Dioxygen: Cytochrome c Oxidase

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Sustaining Life on Planet Earth: Metalloenzymes Mastering Dioxygen and Other Chewy Gases

Part of the book series: Metal Ions in Life Sciences ((MILS,volume 15))

Abstract

Cytochrome c oxidase (CcO) is the terminal oxidase of cell respiration which reduces molecular oxygen (O2) to H2O coupled with the proton pump. For elucidation of the mechanism of CcO, the three-dimensional location and chemical reactivity of each atom composing the functional sites have been extensively studied by various techniques, such as crystallography, vibrational and time-resolved electronic spectroscopy, since the X-ray structures (2.8 Å resolution) of bovine and bacterial CcO have been published in 1995.

X-ray structures of bovine CcO in different oxidation and ligand binding states showed that the O2 reduction site, which is composed of Fe (heme a 3) and Cu (CuB), drives a non-sequential four-electron transfer for reduction of O2 to water without releasing any reactive oxygen species. These data provide the crucial structural basis to solve a long-standing problem, the mechanism of the O2 reduction.

Time-resolved resonance Raman and charge translocation analyses revealed the mechanism for coupling between O2 reduction and the proton pump: O2 is received by the O2 reduction site where both metals are in the reduced state (R-intermediate), giving the O2-bound form (A-intermediate). This is spontaneously converted to the P-intermediate, with the bound O2 fully reduced to 2 O2−. Hereafter the P-intermediate receives four electron equivalents from the second Fe site (heme a), one at a time, to form the three intermediates, F, O, and E to regenerate the R-intermediate. Each electron transfer step from heme a to the O2 reduction site is coupled with the proton pump.

X-ray structural and mutational analyses of bovine CcO show three possible proton transfer pathways which can transfer pump protons (H) and chemical (water-forming) protons (K and D). The structure of the H-pathway of bovine CcO indicates that the driving force of the proton pump is the electrostatic repulsion between the protons on the H-pathway and positive charges of heme a, created upon oxidation to donate electrons to the O2 reduction site. On the other hand, mutational and time-resolved electrometric findings for the bacterial CcO strongly suggest that the D-pathway transfers both pump and chemical protons. However, the structure for the proton-gating system in the D-pathway has not been experimentally identified. The structural and functional diversities in CcO from various species suggest a basic proton pumping mechanism in which heme a pumps protons while heme a 3 reduces O2 as proposed in 1978.

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Acknowledgments

This work is supported by a Grant-in-Aid for the Global Center of Excellence Program (to S. Yoshikawa) and for Scientific Research (A) 2247012 (to S. Yoshikawa), each provided by the Japanese Ministry of Education, Culture, Sports, Science and Technology, and supported by CREST. S. Yoshikawa is “Senior Visiting Scientist in the Riken Harima Institute”.

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Authors and Affiliations

  1. Picobiology Institute, Graduate School of Life Science, University of Hyogo, Kamigohri Akoh Hyogo, 678-1297, Japan

    Shinya Yoshikawa, Atsuhiro Shimada & Kyoko Shinzawa-Itoh

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  1. Shinya Yoshikawa
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Correspondence to Shinya Yoshikawa .

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Editors and Affiliations

  1. Fachbereich Biologie, Universita¨t Konstanz, Konstanz, Germany

    Peter M. H Kroneck

  2. Facultad de Química Departamento de Química Inorganica y Nuc, Universidad Nacional Autónoma de México, Ciudad de México, Distrito Federal, Mexico

    Martha E. Sosa Torres

Abbreviations and Definitions

Abbreviations and Definitions

AN:

bis[3-(dimethylamino)propyl]amine

CcO:

cytochrome c oxidase

CL:

cardiolipin

DCCD:

dicyclohexylcarbodiimide

DCHIm:

1,5-dicyclohexylimidazole

DCU:

dicyclohexyl-N-acyl-urea

DMAP:

4-(dimethylamino)pyridine

D-pathway:

a proton transfer pathway including E242, connecting the negative side with the O2 reduction site

EPR:

electron paramagnetic resonance

FTIR:

Fourier transform infrared

K-pathway:

a proton transfer pathway including K319, connecting the negative side with the O2 reduction site via Y244

heme a :

one of the heme A irons of the A family cytochrome c oxidase, which is in a low-spin state and 6-coordinated in both, the oxidized and reduced states

heme a 3 :

one of the heme A irons of the A family cytochrome c oxidase, which is in a high-spin state and 5-coordinated in the reduced state; this is the site for O2 binding

heme b :

a low-spin heme B iron of bacterial cytochrome c oxidase and quinol oxidase

heme b 3 :

a heme B iron of the C family cytochrome c oxidase, which is in a high-spin state and 5-coordinated in the reduced state; this is the site for O2 binding

heme o 3 :

a heme O iron of bacterial quinol oxidase, which is in a high-spin state and 5-coordinated in the reduced state; this is the site for O2 binding

H-pathway:

a proton transfer pathway including R38 and D51, connecting the negative with the positive side

6LFe:

Cu-depleted form of complex 6LFeCu, see [45]. NMePr=N-methyl-2-propylimidazole-4carboamide, the substituent on o-position of tetraphenylporphyrin (the whole model complex is abbreviated as Fe/Cu[NMePr])

6LFeCu:

a tethered porphyrin complexed with iron and copper. The “6L” indicates that one end of the tethering group is located at the position 6 of one of the 3 pyridine groups coordinated to Cu

OMe:

2,6-di-tert-butyl-4-methoxyphenol

PE:

phosphatidylethanolamine

PG:

phospatidylglycerol

prp:

propionate

ROS:

reactive oxygen species

SDS-PAGE:

sodium dodecyl sulfate polyacrylamide gel electrophoresis

t-Bu:

2,4,6-tri-tert-butylphenol

THF:

tetrahydrofuran

TMPA:

tris(2-pyridylmethylamine)

TMPD:

tetramethyl-p-phenylenediamine

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Yoshikawa, S., Shimada, A., Shinzawa-Itoh, K. (2015). Respiratory Conservation of Energy with Dioxygen: Cytochrome c Oxidase. In: Kroneck, P., Sosa Torres, M. (eds) Sustaining Life on Planet Earth: Metalloenzymes Mastering Dioxygen and Other Chewy Gases. Metal Ions in Life Sciences, vol 15. Springer, Cham. https://doi.org/10.1007/978-3-319-12415-5_4

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