X-Ray Structure of Rhodobacter Capsulatus Cytochrome bc<sub>1</sub>: Comparison with its Mitochondrial and Chloroplast Counterparts

Berry, Edward A.; Huang, Li-Shar; Saechao, L.K.; Pon, Ning G.; Valkova-Valchanova, Maria; Daldal, Fevzi

doi:10.1023/b:pres.0000036888.18223.0e

Cited by 200 publications

(224 citation statements)

References 64 publications

(81 reference statements)

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“…They are 7.5, 8.6, and 10.2 Å, respectively, in the corresponding bovine enzyme. Recently a relative low resolution structure of cytochrome bc 1 complex from Rhodobacter capsulatus was reported (32). The distances obtained among these aromatic amino acids pairs are surprisingly closed to those deduced from the model of the complex of R. sphaeroides.…”

Section: Involvement Of the Phe-195 Of Cytochrome B In Electronmentioning

confidence: 76%

Evidence for Electron Equilibrium between the Two Hemes bL in the Dimeric Cytochrome bc1 Complex

Gong

Xia

et al. 2005

Journal of Biological Chemistry

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The cytochrome bc 1 complex (also known as ubiquinol-cytochrome c reductase or Complex III) is an essential segment of the electron transfer chains of mitochondria and many respiratory and photosynthetic bacteria (1). It catalyzes electron transfer from ubiquinol to cytochrome c with concomitant translocation of protons across the membrane to generate a proton gradient and membrane potential for ATP synthesis. The "proton-motive Q-cycle" is the most favored mechanism for electron and proton transfer in this complex (2, 3). The central feature of the Q-cycle mechanism is the bifurcation of electrons from ubiquinol at the Qo site. The first electron of ubiquinol is transferred to the "high potential chain," consisting of the Rieske [2Fe-2S] cluster, housed in the iron-sulfur protein (ISP), 1 and heme c 1 , housed in cytochrome c 1 . Then the second electron of ubiquinol is passed through the "low potential chain" consisting of heme b L and heme b H , both housed in the cytochrome b subunit.Recently, mitochondrial cytochrome bc 1 complexes from beef (4, 5), chicken (6), and yeast (7) were crystallized, and their three-dimensional structures were determined. The structural information not only supports the Q-cycle mechanism but also suggests the complex functioning as a dimer. This suggestion stems from the following structural data (4 -7): (i) the intertwining of ISPs in the two bc 1 monomers such that the head domain of ISP in one monomer is physically close to and interacting with the cytochrome b and cytochrome c 1 in the 2-fold symmetry-related other monomer; (ii) the presence of two apparently non-communicating cavities in the dimeric complex, each connecting the Qo pocket of one monomer to the Qi pocket of the other; and (iii) the distance between the Fe atoms of the two hemes b L is only 21 Å, which is approximately the same as that between heme b L and b H in one monomer (Fig. 1). The short distance between the two hemes b L and the presence of several aromatic amino acid residues at the interface of the two cytochrome b proteins has promoted investigator to speculate the existence of electron transfer or equilibrating between the two hemes b L (8 -10). Recently the existence of an intertwined dimer in solution was confirmed (11) in the Rhodobacter sphaeroides bc 1 complex through the formation of a four-subunit (two ISPs and two cytochrome bs) adduct by two inter-subunit disulfide bonds between two engineered cysteine pairs: one at cytochrome b and the head domain of ISP and the other at cytochrome b and the tail domain of ISP. However, evidence for inter-monomer b L -b L electron transfer during bc 1 catalysis is still missing, due to the lack of a suitable assay method.It has been reported that during electron transfer through the bc 1 complex, superoxide anion (O 2 . ) is produced (12-18).This results from a leakage of the second electron of ubiquinol, from the low potential chain of the Q cycle electron transfer pathway, to interact with molecular oxygen. The electron-leaking site is thought to be lo...

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Section: Involvement Of the Phe-195 Of Cytochrome B In Electronmentioning

confidence: 76%

Evidence for Electron Equilibrium between the Two Hemes bL in the Dimeric Cytochrome bc1 Complex

Gong

Xia

et al. 2005

Journal of Biological Chemistry

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“…The bacterial cyt bc 1 are typically comprised of three catalytically active subunits that are the cyt b (with two b-type hemes b H and b L ), the cyt c 1 (with a c-type heme) and the iron sulfur (Fe/S) protein with a high potential [2Fe-2S] cluster (1). Comparison of the three dimensional structures of the mitochondrial, chloroplast and bacterial enzymes demonstrate that, despite the reduction of the subunit composition from the eukaryotic counterparts, the bacterial subunits have the same chemically active centers, and also share the same interwoven homodimeric architecture (3,4). In one monomer, the amino terminal trans membrane (TM) anchor of the Fe/S protein subunit lies across the carboxyl terminal TM helix of the cyt c 1 and the loop region connecting the A and B TM helices as well as a portion of the A TM helix of cyt b. Conversely, its membrane external domain bearing the [2Fe-2S] cluster oscillates between the cyt b and cyt c 1 subunits of the opposite monomer (3).…”

mentioning

confidence: 99%

Binding Dynamics at the Quinone Reduction (Q_i) Site Influence the Equilibrium Interactions of the Iron Sulfur Protein and Hydroquinone Oxidation (Q_o) Site of the Cytochromebc₁Complex

2005

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Multiple instances of low potential electron transport pathway inhibitors that affect the structure of the cytochrome (cyt) bc 1 complex to varying degrees, ranging from changes in hydroquinone (QH 2 ) oxidation and cyt c 1 reduction kinetics, to proteolytic accessibility of the hinge region of the iron-sulfur containing subunit (Fe/S protein), have been reported. However, no instance has been documented of any ensuing change on the environment(s) of the [2Fe-2S] cluster. In this work, this issue was addressed in detail by taking advantage of the increased spectral and spatial resolution obtainable with orientation dependent electron paramagnetic resonance (EPR) spectroscopic analysis of ordered membrane preparations. For the first time, perturbation of the low potential electron transport pathway by Q i site inhibitors or various mutations was shown to change the EPR spectra of both the cyt b hemes and the [2Fe-2S] cluster of the Fe/S protein. In particular, two interlinked effects of Q i site modifications on the Fe/S subunit, one changing the local environment of its [2Fe-2S] cluster, and a second affecting the mobility of this subunit are revealed. Remarkably, different inhibitors and mutations at or near the Q i site induce these two effects differently, indicating that the events occurring at the Q i site affect the global structure of the cyt bc 1. Furthermore, occupancy of discrete Q i site subdomains differently impede the location of the Fe/S protein at the Q o site. These findings led us to propose that antimycin A and HQNO mimic the presence of QH 2 and Q at the Q i site, respectively. Implications of these findings in respect to the Q o -Q i sites communications and to multiple turnovers of the cyt bc 1 are discussed. KeywordsAntimycin A; cytochrome bc 1 ; complex III; Rhodobacter capsulatus; photosynthesis and respiration; energy transduction ABBREVIATIONSElectron paramagnetic resonance (EPR); [2Fe-2S] cluster containing protein (Fe/S); quinone (Q); cytochrome b (cyt b); hydroquinone (QH 2 ); hydroquinone:cytochrome (cyt) c oxidoreductase (cyt bc 1 ); 2-heptyl-4-hydroxyquinoline N-oxide (HQNO); 2-nonyl-4-hydroxyquinoline N-oxide (NQNO); quinone reduction site (Q i ); hydroquinone oxidation site (Q o ) *To whom correspondence should be addressed: Phone: (215) 898-4394 Fax: (215) 898-8780 E-mail:fdaldal@sas.upenn.edu. This work was supported by NIH grant R01 GM 38237 to F. D. and NIH F32 GM 65791 and AHA #0425515U fellowships to J. W. C. NIH Public Access Author ManuscriptBiochemistry. Author manuscript; available in PMC 2006 February 2. Published in final edited form as:Biochemistry. 2005 August 9; 44(31): 10520-10532. NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author ManuscriptThe hydroquinone (QH 2 ):cytochrome (cyt) c oxidoreductase (cyt bc 1 ) is an essential component of the mitochondrial and most bacterial respiratory electron transport pathways (1). A sister complex, the cyt b 6 f, is also a part of the photosynthetic electron transport chains of the chloroplasts of highe...

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“…The complex catalyzes oxidation of substrate ubiquinol (QH 2 ) by a watersoluble ferricytochrome c 2 in the periplasmic space and generates a proton-motive force for ATP synthesis through a Q-cycle mechanism (1,2). With the availability of structures from mitochondrial and bacterial systems (3)(4)(5)(6)(7)(8), the mechanism could be further refined. Proteins of the bc 1 complex family form homodimers inserted in the cellular or mitochondrial membrane, each monomer containing minimally the three subunits (cyt b with two b-type hemes (b H and b L ), cyt c 1 with heme c 1 , and Rieske-type iron-sulfur protein (ISP)) that form the catalytic core of the complex.…”

mentioning

confidence: 99%

“…The bacterial structures are much simpler than the 8 -11 subunit complexes in mitochondria. The isolated complex has four subunits in each monomer (cyt b, cyt c 1 , ISP, and subunit IV) (9,10), but crystallographic structures of the bc 1 complex from Rhodobacter species show only the three catalytic subunits (6,7), leaving some uncertainty as to the role of subunit IV. The R. sphaeroides system provides a convenient model for mitochondrial systems because flash activation through the RC initiates turnover, and kinetics can then be measured spectrophotometrically.…”

mentioning

confidence: 99%

Modifications of Protein Environment of the [2Fe-2S] Cluster of the bc1 Complex

Lhee

Kolling

Nair

et al. 2010

Journal of Biological Chemistry

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The rate-determining step in the overall turnover of the bc 1 complex is electron transfer from ubiquinol to the Rieske ironsulfur protein (ISP) at the Q o -site. Structures of the ISP from Rhodobacter sphaeroides show that serine 154 and tyrosine 156 form H-bonds to S-1 of the [2Fe-2S] cluster and to the sulfur atom of the cysteine liganding Fe-1 of the cluster, respectively. These are responsible in part for the high potential (E m,7 ϳ300 mV) and low pK a (7.6) of the ISP, which determine the overall reaction rate of the bc 1 complex. We have made site-directed mutations at these residues, measured thermodynamic properties using protein film voltammetry to evaluate the E m and pK a values of ISPs, explored the local proton environment through two-dimensional electron spin echo envelope modulation, and characterized function in strains S154T, S154C, S154A, Y156F, and Y156W. Alterations in reaction rate were investigated under conditions in which concentration of one substrate (ubiquinol or ISP ox ) was saturating and the other was varied, allowing calculation of kinetic terms and relative affinities. These studies confirm that H-bonds to the cluster or its ligands are important determinants of the electrochemical characteristics of the ISP, likely through electron affinity of the interacting atom and the geometry of the H-bonding neighborhood. The calculated parameters were used in a detailed Marcus-Brønsted analysis of the dependence of rate on driving force and pH. The proton-first-then-electron model proposed accounts naturally for the effects of mutation on the overall reaction.Enzymes of the cytochrome bc 1 complex 2 family (EC 1.10.2.2) are ubiquitous membrane proteins in mitochondria and bacteria (and, including the b 6 f complex, in chloroplasts) that play a central role in the electron transfer chains of respiration and photosynthesis. In Rhodobacter sphaeroides, the bc 1 complex, together with the reaction center (RC) and cytochrome (cyt) c 2 , forms the photosynthetic chain. The complex catalyzes oxidation of substrate ubiquinol (QH 2 ) by a watersoluble ferricytochrome c 2 in the periplasmic space and generates a proton-motive force for ATP synthesis through a Q-cycle mechanism (1, 2). With the availability of structures from mitochondrial and bacterial systems (3-8), the mechanism could be further refined. Proteins of the bc 1 complex family form homodimers inserted in the cellular or mitochondrial membrane, each monomer containing minimally the three subunits (cyt b with two b-type hemes (b H and b L ), cyt c 1 with heme c 1 , and Rieske-type iron-sulfur protein (ISP)) that form the catalytic core of the complex. The ␣-proteobacterial ancestors of mitochondria were likely derived from photosynthetic progenitors, accounting for the high degree of homology in sequence, structure, and mechanism. The bacterial structures are much simpler than the 8 -11 subunit complexes in mitochondria. The isolated complex has four subunits in each monomer (cyt b, cyt c 1 , ISP, and subunit IV) (9, 10), but crystallo...

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X-Ray Structure of Rhodobacter Capsulatus Cytochrome bc₁: Comparison with its Mitochondrial and Chloroplast Counterparts

Cited by 200 publications

References 64 publications

Evidence for Electron Equilibrium between the Two Hemes bL in the Dimeric Cytochrome bc1 Complex

Evidence for Electron Equilibrium between the Two Hemes bL in the Dimeric Cytochrome bc1 Complex

Binding Dynamics at the Quinone Reduction (Q_i) Site Influence the Equilibrium Interactions of the Iron Sulfur Protein and Hydroquinone Oxidation (Q_o) Site of the Cytochromebc₁Complex

Modifications of Protein Environment of the [2Fe-2S] Cluster of the bc1 Complex

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X-Ray Structure of Rhodobacter Capsulatus Cytochrome bc1: Comparison with its Mitochondrial and Chloroplast Counterparts

Cited by 200 publications

References 64 publications

Evidence for Electron Equilibrium between the Two Hemes bL in the Dimeric Cytochrome bc1 Complex

Evidence for Electron Equilibrium between the Two Hemes bL in the Dimeric Cytochrome bc1 Complex

Binding Dynamics at the Quinone Reduction (Qi) Site Influence the Equilibrium Interactions of the Iron Sulfur Protein and Hydroquinone Oxidation (Qo) Site of the Cytochromebc1Complex

Modifications of Protein Environment of the [2Fe-2S] Cluster of the bc1 Complex

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X-Ray Structure of Rhodobacter Capsulatus Cytochrome bc₁: Comparison with its Mitochondrial and Chloroplast Counterparts

Binding Dynamics at the Quinone Reduction (Q_i) Site Influence the Equilibrium Interactions of the Iron Sulfur Protein and Hydroquinone Oxidation (Q_o) Site of the Cytochromebc₁Complex