The bc1-complex

Complex III


Name

Formal name: ubiquinol:cytochrome c oxidoreductase
Trivial name: bc1-complex (bc-complex)
Alternative name: Complex III

Function

The formal name describes the function: the enzyme oxidizes ubiquinol (ubihydroquinone) which reacts from the membrane phase, reduces cytochrome c in the intermembrane space (or periplasm in bacteria), and uses the free energy change to transport 2 (vectorial) H+/QH2 across the membrane from matrix (N side) to inter membrane space (P side), and release 2 additional (scalar) H+/QH2 into the inter membrane space.
QH2 + 2 ferricyt c3+ + 2H+N <==> Q + 2 ferrocyt c2+ + 4H+P

Mechanism

The bc1-complex works through a modified Q-cycle mechanism. The link has details of the reaction mechanism as determined for the enzyme in the photosynthetic chain of Rb. sphaeroides. In addition, physico-chemical data for redox parameters, rate constants, etc., which describe the mechanism are given.

The Q-cycle mechanism is summarized in the following Scheme:

The scheme shows the Q-cycle in the context of the structure. The catalytic subunits are shown by their surfaces, made transparent so as to reveal the redox centers. The reactions are catalyzed by three subunits; cyt b (cyan), containing two b-type hemes, bL (lower potential heme) and bH (higher potential heme); cyt c1 (blue), containing heme c1; and the iron sulfur protein (yellow), containing an Fe2S2 center. Quinol is oxidized at the Qo-site of the complex. The reaction is rate determining and has a relatively high activation barrier. Quinol oxidation occurs in a bifurcated reaction, in which one electron is transferred to a high potential chain and the other to a low potential chain. The high potential chain, consisting of the ISP, cyt c1 and cyt c (or c2) (red), transfers the first electron from quinol to an acceptor (cytochrome oxidase in mitochondria, the oxidized photochemical reaction center in photosynthetic systems), leaving a semiquinone at the Qo-site. Because the semiquinone formed is unstable, and undetectable during normal turnover, the reaction at the Qo-site appears to be a concerted electron transfer to the high and low potential chains. The low potential chain consists of two cyt b hemes (cyt bL and cyt bH, for low and higher potential hemes), which serve as a pathway through which electrons are transferred across the coupling membrane from semiquinone at the Qo-site to the Qi-site, at which quinone is reduced to quinol. In order to provide the two electrons at the Qi-site required for reduction of quinone, the Qo-site oxidizes two equivalents of quinol in successive turnovers. The first electron at the Qi-site generates a relatively stable semiquinone which is reduced to quinol by the second electron. The integration of the oxidation and reduction reactions with the release or uptake of protons in the aqueous phases, allows the complex to pump protons across the membrane. Electron transfer between the two Q-sites through the b-cytochrome chain provides the electrogenic work.

You can download several "working models" of the complex. A "do-it-yourself" model of the bacterial photosynthetic electron transfer chain , using a template and coins to represent the quinones, electrons and protons, is the simplest version. An animated gif version of this shows the model in action (be patient when linking to this page, because the full model will take a while to load). A more recent annotated working model based on the crystallographic structures, and on suggestions from the Crofts Lab for a molecular mechanism, is shown here in a 3-D movie.

Subunit composition

The bc1-complex from beef heart mitochondria

Subunit (no.)   Redox centers           Mr(beef)        Function

Core I          none                    53.6            No catalytic, protein transport
Core II         none                    46.5            No catalytic, protein transport
Cyt b (III)     heme bH                 42.6            donor to Qi-site
                heme bL                                 acceptor from SQ at Qo-site
                                                        Transmembrane electron transfer
Cyt c1(IV)      heme c1                 27.3            donor to cyt c
Rieske (V)      2Fe.2S center           21.6            acceptor from QoH2
                                                        donor to cyt c1
Subunit VI      none                    13.3            none known
Subunit VII     none                    9.5             none known
Subunit VIII    none                    9.2             hinge protein (interacts with c1)
Subunit IX      none                    8.0             none known
Subunit X       none                    7.2             none known
Subunit XI      none                    6.4             none known (not present in chicken)

The bc1-complex from Rhodobacter sphaeroides

Cyt b (I)       heme bH                 50              donor to Qi-site
                                                        Acceptor of electrons from heme bL
                heme bL                                 acceptor from SQ at Qo-site
                                                        Transmembrane electron transfer
Cyt c1(II)      heme c1                 28.6            donor to cyt c
Rieske (III)    2Fe.2S center           19.9            acceptor from QoH2
                                                        donor to cyt c1
Subunit IV      none                    14.4            may contribute to Qo-site

Sequence information

Sequences for all subunits of the beef heart mitochondrial complex have been compiled by Ed Berry,- other sequences are accessible from Ed's home page.

Click on these links for alignments of sequences from many mitochondrial, and some bacterial bc1-complexes.

The structure of the bc1-complex

Structures of the bc1 complex from mitochondria have been published by three groups, the first from a collaboration between Diesenhofer's group and Chang-An Yu's group (Xia et al., 1997) (1), and from Berry's group in Kim's laboratory (Zhang et al., 1998) (2). More recently, additional structures of the beef complex have been published by Iwata et al. (16), and a higher resolution structure of the yeast complex has been described by Hunte and Michel (17). All complexes so far solved are dimeric, showing a two-fold symetry about an axis vertical to the membrane plane; all groups report crystals with a homodimer containing two bc1-complex monomers with a subunit composition as described in the table above. There is enough interdigitation between monomers to suggest that dissociation of the dimer would be unlikely. It therefore seems probable that the complex is structurally dimeric in its native state.

Structures of mitochondrial complexes from beef, chicken, yeast, and rabbit (including, in the case of Berry's chicken complex, several different structures with different inhibitors in place), have been solved by several laboratories (see refs. below). The structure of the native chicken heart mitochondrial complex from Ed Berry's work (Zhang et al., 1998) (2) is shown here:

Click thumbnail for larger version

General features

The general features of the protein are as expected from previous biochemical and structural studies, with a large fraction corresponding to the "core" proteins (subunits I and II) on the N-side (bottom in the Fig. above), and cyt c1 and the FeS protein on the P-side. The dimensions of the dimer are about 130 Å in diameter and 151 Å in height, with the inter-membrane space region, the transmembrane region, and the matrix region contributing about 41 Å, 35 Å and 75 Å respectively.

Prosthetic groups

The prosthetic group composition is as expected from biochemical studies: cyt bL, cyt bH, cyt c1, 2Fe.2S center.
Cyt bL --> cyt bH distance is 20 Å (13 Å edge to edge), perpendicular to membrane. Assuming that cyt bH is close to the antimycin binding site, the arrangement in the protein is as expected from models based on mechanistic studies and structural prediction.
The positions of the heme centers are essentially the same in all structures. The cyt bL hemes of the two monomers are 21 Å apart in the dimer, the cyt bH hemes are 33 Å apart, and the cyt c1 hemes are 53 Å apart.

In the Xia et al. structure (1, not shown), the protein of the iron sulfur protein (ISP) was not resolved, because of disorder; the cyt c1 subunit was only partly resolved. The position of the 2Fe.2S center was determined, with the following distances:
Cyt L --> 2Fe.2S distance is 26 Å.
2Fe.2S --> cyt c1 distance is 31 Å
the FeS centers are 63 Å apart.

In the Zhang et al. (2) structure, both the ISP and cyt c1 were well resolved, but showed different distances between the Fe-centers in the native crystals:
Cyt L --> 2Fe.2S distance is 34.3 Å.
2Fe.2S --> cyt c1 distance is 21.3 Å
When the structure of crystals containing the Qo-site inhibitor stigmatellin were solved (2), the position of the ISP had changed so as to be close to that inferred from the Xia et al. (1) distances. Distances between the Fe-centers in the stigmatellin crystals were:
Cyt L --> 2Fe.2S distance is 26.4 Å.
2Fe.2S --> cyt c1 distance is 31.6 Å

Zhang et al. (1) and Crofts et al. (3) have suggested that the two different positions reflect a domain movement which is essential for catalysis, since in neither of the positions observed would the complex be fitted for catalysis of all the partial reactions of quinol oxidation.

Spatial considerations

The biggests surprise from the earlier Xia et al. (1) structure was the distance between the 2Fe.2S center and cyt c1. The kinetic data suggest that this reaction is rapid, with t½ < 10 µs. The distance of 31 Å observed in the Xia et al. structures would not permit this rate. The distances between centers in Berry's native structures (2) are similar to those in the Xia/Deisenhofer/Yu structure, except for the position of the 2Fe.2S centers. These are closer to cyt c1, and further from heme bL. These differences have led us to suggest that the extrinsic domain of the Rieske ISP containing the 2Fe.2S center (the mobile head) must move relative to the other two catalytic subunits, by a rotational displacement of ~22 Å. The movement of the ISP head brings the 2Fe.2S cluster from a position close to cyt c1 to a concave interface on cyt b at which it is close to the quinol binding site (the Qo-site). In the presence of stigmatellin, the contact seen in electron density maps can be modeled as a H-bond between Ne of His-161 (a ligand to the 2Fe.2S center), and a carbonyl O-atom of the stigmatellin ring (2).

There are 13 transmembrane helices apparent in the X-ray structure. Eight of these belong to cyt b (SUIII), as in models based on structural prediction. The remaining four helices are assigned to the remaining subunits, one each coming from cyt c1 (SUIV), ISP (SUV), SUVII and SUX) (1, 2).

In addition to the transmembrane helices, cytochrome b has five prominent helices outside the membrane, and parallel to the membrane plane. These correspond to amphipathic helices a, ab, cd, and ef predicted from sequence analysis, with the cd span forming two helices, cd1 and cd2 in a hairpin, with a turn at the conserved proline. The arrangement of transmembrane helices around the hemes, and the contributions of transmembrane and amphipathic helices to the quinone binding sites are much as predicted from model studies.

The present coordinates from the Xia et al. (1) complex from beef heart mitochondria are from diffraction data to 2.8 Å. A native data set, has been deposited with the Protein Data Bank as file 1qcr. Data sets with inhibitors (antimycin, myxothiazol, stigmatellin or UHDBT) bound have been solved, but not yet deposited.
The data from Zhang et al. (2) are from the chicken heart mitochondrial complex at 3.0 Å resolution, and coordinates for the native structure, and the complex co-crystallized with stigmatellin and antimycin, have been deposited with the Protein Data Bank, as files 1bcc and 3bcc. Additional structures for the chicken complex in co-crystals with stigmatellin alone (deposited as 2bcc), myxothiazol, antimycin alone, UHDBT, and several MOA-type inhibitors are also solved, and coordinates for some of these are available through the bc1 complex home page.
Berry's group have also solved structures for complexes from the heart mitochonria of rabbit, and two different complexes from beef, at slightly lower resolution.
Structures from the Iwata group are deposited as files 1be3 (P6522 crystals) and 1bgy (P65 crystals).

Inhibitor binding

The antimycin binding site is close to a b-heme, assigned as cyt bH on the basis of biophysic evidence. From the Xia et al. work (1), the difference electron density map ± antimycin showed a strongly defined density for the inhibitor, and a loss of density which probably corresponds to a displaced ubiquinone. Zhang et al. (2) modeled density in the native structure as quinone at the Qi-site, and this density was lost in antimycin co-crystals.

The Qo-site shows a bifurcated binding pocket (1, 2). The UHDBT (or stigmatellin) binding domain is close to the 2Fe.2S center in a lobe distal from cyt bL. The myxothiazol (or MOA-type inhibitors) binding site is further away from the ISP binding interface, in a lobe proximal to heme bL. The tails of the inhibitors reach out into the putative lipid domain, though a relatively narrow orifice which has a cross-sectional area similar to the tails (3). As a consequence, the binding domains overlap, and the site would not be expected to accommodate both types of inhibitor at the same time. This provides a structural basis for the earlier observation from biophysical studies that occupation by UHDBT and myxothiazol, or stigmatellin and myxothiazol, is mutually exclusive.

In the Zhang et al. work (2), a weak electron density at the Qo-site in the native structure may represent weakly bound quinone. The strong occupancy expected at the site from the double-occupancy hypothesis of Ding and Dutton (4) is not found in any of the structures from either group. Crofts et al. (3) have suggested that the two lobes of the Qo-site are occupied by different intermediates of the quinl oxidation reaction. The suggestion is based on the bifurcated nature of the Qo-site, the failure to detect a strongly binding quinone, the different domains of the two types of inhibitor, and the differential effects of mutation on inhibitor binding and the interaction of quinone with the ISP detected through the gx=1.800 EPR band. They suggest that the quinol bound in the distal lobe forms a reaction intermediate with ISPox, which leads to electron transfer to form the semiquinone, and that the semiquinone must move to the proximal site before oxidation by cyt bL.

Arrangement of the prosthetic groups - based on the Zhang et al. structure of the chicken heart mitochondrial complex, with antimycin and stigmatellin (PDB file 3bcc).

Colors are:
Monomer 1: cyt bH, green-blue, (top) and cyt bL, dark green; FeS, orange; cyt c1, yellow
Monomer 2: cyt bH, blue, (top) and cyt bL, dark blue; FeS, red; cyt c1, pale blue
Both monomers: antimycin, cyan; stigmatellin, magenta.
Note that the head group of ISP from monomer 1 (containing the orange FeS center) interacts with the Qo-site associated with cyt bL (blue), and with cyt c1 (paleblue), of monomer 2, and vice versa.

The bc1 complex in a Chime tutorial.

You will need Netscape 3.0 or higher, and Chemscape Chime 1.0 or higher, to see the model within your viewer

You can download Chime by clicking here.  Chime plug-in

Other structural studies

Smith, Cramer and colleagues (5) have previously reported a high resolution structure for a solubilized cyt f of the b6f-complex from higher plants, and Berry et al. (6) have reported a similar structure from Chlamydomonas. A low resolution structure for the complete complex has been reported by Mosser et al. (7). Iwata, Michel, Link and colleagues have recently reported on a high resolution structure for the solubilized Rieske FeS protein from the beef heart complex (8), and Carrell et al. for the chloroplast Rieske protein (9).

Structure references

  1. Di Xia, Chang-An Yu, Hoeon Kim, Jia-Zhi Xia, Anatoly M. Kachurin, Li Zhang, Linda Yu, Johann Deisenhofer. Crystal Structure of the Cytochrome bc1 Complex from Bovine Heart Mitochondria. Full text, or Abstract.
  2. Z. Zhang, L. Huang, V. M. Shulmeister, Y.-I. Chi, K.-K. Kim, L.-W. Hung, A. R. Crofts, E. A. Berry & S.-H. Kim. Electron transfer by domain movement in cytochrome bc1 Nature 392, 677 (1998). Abstract.
  3. Crofts, A.R. and Berry, E.A. (1998) Structure and function of the cytochrome bc1 complex of mitochondria and photosynthetic bacteria. Curr. Opinions in Struc. Biol. 8, 501-509. Abstract, Full text, or reprint (PDF format).

  4. Crofts, A.R., Guergova-Kuras, M., Huang, L.-S., Kuras, R., Zhang, Z. and Berry, E.A.(1999) The mechanism of ubiquinol oxidation by the bc1 complex: the role of the iron sulfur protein, and its mobility. Biochemistry 38, 15791-15806. Request a preprint

  5. Crofts, A.R., Barquera, B., Gennis, R.B., Kuras, R., Guergova-Kuras, M. and Berry, E.A. Mechanistic aspects of the Qo-site of the bc1-complex as revealed by mutagenesis studies, and the crystallographic structure. (Crofts, Berry et al.) Abstract or Full text.
  6. Crofts, A.R., Hong, S.J., Ugulava, N., Barquera, B., Gennis, R.B., Guergova-Kuras, M., and Berry, E. (1999) Pathways for proton release during ubihydroquinone oxidation by the bc1 complex. Proc. Natl. Acad. Sci. U.S.A., 96, 10021-10026. Reprint (PDF format)
  7. Crofts, A.R., Hong, S., Zhang, Z. and Berry, E.A. (1999) Physicochemical aspects of the movement of the Rieske iron sulfur protein during quinol oxidation by the bc1 complex. Biochemistry 38, 15827-15839. Request a preprint
  8. Crofts, A.R., Barquera, B., Gennis, R.B., Kuras, R., Guergova-Kuras, M. and Berry, E.A. (1999) The mechanism of ubiquinol oxidation by the bc1 complex: the different domains of the quinol binding pocket, and their role in mechanism, and the binding of inhibitors. Biochemistry 38, 15807-15826. Request a preprint
  9. Hong, S.J., Ugulava, N., Guergova-Kuras, M., and Crofts, A.R. (1999) The energy landscape for ubihydroquinone oxidation at the Qo-site of the bc1 complex in Rhodobacter sphaeroides. J. Biol. Chem. 274: 33931-33944. Request a preprint, or Download an interactive program to explore Marcus curves for Qo electron transfer reactions
  10. Ding, H., Daldal, F. and Dutton, P.L. (1995) Biochemistry 34, 15997-16003
  11. Martinez, S.E., Huang, D., Szczepaniak, A., Cramer, W.A. and Smith, J.L.(1994) Crystal structure of the chloroplast cytochrome f refeals a novel cytochrome fold and unexpected heme ligation. Structure 2, 95-105).
  12. Berry, E.A., Huang, L.-S., Chi, Y., Zhang, Z., Malkin, R. and Fernandez-Velasco, J.G. (1997) Biophysical J. 72, Abstr A125.
  13. Mosser, G., Breyton, C., Olofsson, A., Popot, J.-L. and Rigaud, J.-L. (1997) Projection map of cytochrome b6f complex at 8 Å resolution. J. Biol. Chem. 272, 20263-20268.
  14. Iwata, S., Saynovits, M., Link, T.A. and Michel, H. (1996) Structure of a water soluble fragment of the 'Rieske' iron-sulfur protein of the bovine heart mitochondrial cytochrome bc1 complex determined by MAD phasing at 1.5Å resolution. Structure 4, 567-579.
  15. Carrell, C.J., Zhang, H.M., Cramer, W.A. and Smith, J,L. (1998) Biological identity and diversity in photosyntheris and respiration - structure of the lumen-side of the chloroplast Rieske protein. Structure, 5(12), 1613-1625.
  16. So Iwata, Joong W. Lee, Kengo Okada, John Kyongwon Lee, Momi Iwata, Bjarne Rasmussen, Thomas A. Link, S. Ramaswamy, Bing K. Jap (1998) Complete Structure of the 11-Subunit Bovine Mitochondrial Cytochrome bc1 Complex. Abstract or Full TextScience, 281, 64-71
  17. Hunte C., Koepke J., Lange C., Rossmanith T., and Michel H. (2000) Structure at 2.3 angstrom resolution of the cytochrome bc1 complex from the yeast Saccharomyces cerevisiae co-crystallized with an antibody Fv fragment. Structure with Folding & Design. 8, 669-684

View of a model structure for cytochrome b from Rb. sphaeroides

The crystallographic structures have provided a nice validation of structural models derived from sequence analysis, mutational studies, characterization of the electrogenic reactions of te complex, and biophysical models of the mechanism. View a model of cytochrome b from this earlier work in Chime.

The bc1-complex home page

A comprehesive set of information can be found at the bc-complex site, and the various links available from those pages. 
©Copyright 1996, Antony Crofts, University of Illinois at Urbana-Champaign, a-crofts@uiuc.edu