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Structural basis for the mechanism of electron bifurcation at the quinol oxidation site of the cytochrome bc 1 complex

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Abstract

At the heart of the Q cycle hypothesis, the cytochrome bc 1 complex (bc 1) is required to separate the two electrons from a quinol molecule at the quinol oxidation site. Recent studies have brought to light an intricate mechanism for this bifurcated electron transfer. A survey of the protein data bank shows 30 entries for the structures of bc 1 and the homologous b 6 f complex. These structures provide considerable insights into the structural organization of mitochondrial, bacterial, and plant enzymes. Crystallographic binding studies of bc 1 with either quinone reduction (QN) and/or quinol oxidation (QP) site inhibitors offer atomic details on how these compounds interact with residues at their respective sites. Most importantly, the different locations and apparent flexibility observed in crystals for the extrinsic domain of the iron-sulfur protein (ISP) subunit suggest a mechanism for electron bifurcation at the QP site. Analyses of various inhibitor-bound structures revealed two classes of QP site inhibitors: Pm inhibitors that promote ISP mobility and Pf inhibitors that favor the fixation of the ISP conformation. Those analyses also shed light on a possible process by which the ISP motion switch is controlled. The first phase reduction of ISP is shown to be comparable to the reduction of the b L heme by pre-steady state kinetic analysis, whereas the second phase reduction of ISP share similar kinetics with the reduction of the b H heme. The reduction of cyt c 1 is measured much slower, indicating that the reduced ISP remains bound at the QP site until the reduced heme b L is oxidized by the heme b H and supporting the existence of a control mechanism for the ISP motion switch.

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Abbreviations

2Fe2S :

Two-iron-two-sulfur cluster of ISP

bc 1 :

Ubiquinol cytochrome c oxidoreductase

b H :

High potential b heme

b L :

Low potential b heme

cyt b :

Cytochrome b subunit

cyt c 1 :

Cytochrome c 1 subunit

EPR:

Electron paramagnetic resonance

ET:

Electron transfer

IMS:

Intermembrane space

ISP:

Iron-sulfur protein subunit

ISP-ED:

The extrinsic domain of ISP

MOA:

β-Methoxyacrylate

NQNO:

2-Nonyl-4-hydroxyquinoline N-oxide

Pf:

Quinol oxidation site inhibitors that fix ISP-ED conformation

Pm:

Quinol oxidation site inhibitors that promote ISP-ED movement

QP :

Quinol oxidation

QN :

Quinone reduction

QH2 :

Ubiquinol

rms deviation:

Root mean square deviation

Rsbc 1 :

Rhodobacter sphaeroides bc 1

TM:

Transmembrane

UHDBT:

5-Undecyl-6-hydroxy-4,7-dioxobenzothiazol

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Acknowledgments

This research was supported in part by the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research, and in part from a NIH grant (GM 30721) to CAY. The authors wish to thank George Leiman for editorial assistance.

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Authors and Affiliations

  1. Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, NIH, 37 Convent Dr., Building 37, Room 2122C, Bethesda, MD, 20892, USA

    Di Xia & Lothar Esser

  2. Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA

    Linda Yu & Chang-An Yu

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  1. Di Xia
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  2. Lothar Esser
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  3. Linda Yu
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  4. Chang-An Yu
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Correspondence to Di Xia or Chang-An Yu.

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Xia, D., Esser, L., Yu, L. et al. Structural basis for the mechanism of electron bifurcation at the quinol oxidation site of the cytochrome bc 1 complex. Photosynth Res 92, 17–34 (2007). https://doi.org/10.1007/s11120-007-9155-3

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  • DOI: https://doi.org/10.1007/s11120-007-9155-3

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