Structural analysis of cytochrome bc1 complexes: implications to the mechanism of function

Abstract

The cytochrome bc1 complex (bc1) is the mid-segment of the cellular respiratory chain of mitochondria and many aerobic prokaryotic organisms; it is also part of the photosynthetic apparatus of non-oxygenic purple bacteria. The bc1 complex catalyzes the reaction of transferring electrons from the low potential substrate ubiquinol to high potential cytochrome c. Concomitantly, bc1 translocates protons across the membrane, contributing to the proton-motive force essential for a variety of cellular activities such as ATP synthesis. Structural investigations of bc1 have been exceedingly successful, yielding atomic resolution structures of bc1 from various organisms and trapped in different reaction intermediates. These structures have confirmed and unified results of decades of experiments and have contributed to our understanding of the mechanism of bc1 functions as well as its inactivation by respiratory inhibitors. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.

Keywords: Bifurcated electron flow; Bos taurus bc(1); Btbc(1); CA; CL; Control of ISP domain movement; Crystal structure; Cytochrome bc(1) complex; ET; Gallus gallus bc(1); Ggbc(1); ISC; ISP; ISP-ED; MPP; Mechanism of ubiquinol oxidation; Mtbc(1); NCS; Non-crystallographic symmetry; PC; PDB; PE; PI; Q; Q(N); Q(P); QH(2); SC; Scbc(1); TM; b(H); b(L); bc(1); bc(1) from Saccharomyces cerevisiae; cardiolipin; complex III or ubiquinol cytochrome c oxidoreductase or cytochrome bc(1); contact area; electron transfer; extrinsic domain of ISP; from Rhodobacter sphaeroides; high-potential heme or b(562); iron–sulfur cluster; iron–sulfur protein; low-potential heme or b(566); mitochondrial bc(1); mitochondrial processing peptidase; phosphatidylcholine; phosphatidylethanolamine; phosphatidylinositol; protein data bank; rms deviation; root-mean-square deviation; surface complementarity; transmembrane; ubiquinol; ubiquinol oxidation,Rsbc(1); ubiquinone; ubiquinone reduction.

Figure 1. Crystal structures in ribbon representation for mitochondrial and bacterial bc₁ complexes

(A) Structural model of the dimeric bc₁ complex from bovine mitochondria. The eleven different subunits are represented as ribbons with the color codes and subunit designations given on the left. Prosthetic groups such as the hemes b_L, b_H, and c₁ are shown as stick models. The Iron-sulfur clusters are shown as van der Waals sphere models. The two black horizontal lines delineate the boundaries of the membrane bilayer. The three regions of the bc₁ complex are indicated as IMS (intermembrane space), TM (transmembrane) and Matrix regions, respectively. (B) Structural model of the photosynthetic bacterium R. sphaeroides bc₁. Color codes for Rsbc₁ are the same as those for Btbc₁ except those in red, which represent insertions in cyt b, cyt c₁ and ISP subunits in relation to the corresponding subunits in Btbc₁. (C) Positions of and distances between iron atoms of prosthetic groups. Hemes b_L, b_H and c₁ as well as 2Fe-2S clusters are labeled. Arrowed lines indicate low and high potential chains for ET. (D) Ribbon diagram showing the structure of monomeric bovine cyt b. Eight TM helices are labeled. The two b-type hemes b_L and b_H are shown as stick models. The axial histidine ligands to the heme groups are also shown as stick models and labeled. The two conserved and functionally important motifs, the cd1 helix and the PEWY sequence, are shown in magenta and cyan, respectively, and as labeled. (E) Ribbon presentation of the structure of bovine cyt c₁. Btcyt c₁ has its N- and C-terminus on the positive and negative sides of the membrane, respectively. The heme c₁ along with its two axial ligands ^BtM160 and ^BtH41 are shown as stick models. (F) Ribbon diagram showing the structure of the bovine ISP subunit. The N-terminus of the ISP is on the negative side of the membrane, whereas the C-terminus is on the positive side. The 2Fe-2S cluster is shown as spheres; the two histidine ligands H141 and H161 for the ISC are shown as stick models and are labeled. The flexible linker or neck between the TM helix and the ISP-ED is shown as a loop in magenta. (G) Ribbon diagram of the structure of Rscyt b. Structural features of the subunit are similarly labeled as those in Btcyt b except for the insertions, which are shown in red. Histidine ligands to the hemes b_L (H97 and H198) and to b_H (H111 and H212) are shown as stick models. (H) Ribbon representation of the structure of Rscyt c₁. Structural features of the subunit are similarly labeled as those in Btcyt c₁ except for the insertions, which are shown in red. Heme c₁ ligands are given as stick models for M185 and H40. (I) Ribbon diagram showing the structure of RsISP. Structural features of the subunit are similarly labeled as those in BtISP except for the insertions, which are shown in red. Histidine ligands to the RsISC are show as stick models for H131 and H152.

Figure 2. Q-cycle mechanism

The Q cycle mechanism defines two reaction sites: quinol oxidation (Center P or Q_P) and quinone reduction (Center N or Q_N). It takes two quinol oxidation cycles to complete. At first, a QH₂ moves into the Q_P site and undergoes oxidation with one electron going to cyt c via the ISP and cyt c₁ (high-potential chain), and another ending in the Q_N via hemes b_L and b_H (low-potential chain) to form a ubisemiquinone, and releasing its two protons to the Φ⁺ site of the membrane. The second QH₂ is oxidized in the same way at the Q_P site but its low potential chain electron ends up reducing the ubisemiquinone radical. Reduced QH₂ is released upon picking up two protons from the negative side of the membrane. As a result of the Q cycle, 4 protons are transferred to the Φ⁺ side, 2 protons are picked up from the Φ⁻ side and effectively only one QH₂ molecule is oxidized.

Figure 3. Binding of substrate, inhibitor and lipid molecules to the cyt bc₁ complex

(A) Hydrogen bonding interaction between stigmatellin and the ISP. In this figure, much of the protein structures of cyt b and ISP are omitted for clarity to illustrate the H-bond between stigmatellin and the ISC. All residues, the ISC, and stigmatellin are shown as ball-and-stick models and as labeled. The distance between ^BTH161, one of the 2Fe-2S ligand, and stigmatellin is shown as 2.8 Å. (B) No hydrogen bonding is observed between famoxadone and the ISP. Binding of famoxadone arrests the ISP-ED motion. But the closest distance between ^BTH161 and the ISP is >6 Å. (C) Interaction of the protein environment at the Q_N site of the cyt b subunit with bound substrate ubiquinone with two isoprenoid repeats. Secondary structure elements surrounding the Q_N pocket, including portions of the N-terminal helix a, TM helices A, D, and E, and extra-membrane loops A and DE, are shown and are labeled. Residues interacting with bound substrate and the b_H heme are drawn in stick models and are labeled with carbon atoms in yellow, nitrogen in blue, oxygen in red, and iron in orange. H-bonds are indicated with pinkish dotted lines. Water molecules are shown as isolated red balls. The residues that are with magenta labels confer inhibitor resistance. The substrate ubiquinone, caged in Fo-Fc electron densities calculated with refined phases after ligand being omitted and contoured at the 3σ level in dark green, are drawn as ball-and-stick models with carbon atoms in black, nitrogen in light blue, and oxygen in red. Additionally, the two bound water molecules are enclosed in the Fo-Fc electron density in cyan calculated with refined phases obtained with the waters omitted and contoured at 3σ. (D) Binding environment of the bound lauryl oleoyl phosphatidyl ethanolamine (PE) in the structure of Rsbc₁. The modeled lipid is located near the N-side and its binding environment is shown.

Figure 4. Control of the ISP-ED motion switch and the proposed mechanism for bifurcation of electron flow at the Q_P pocket

The structural components necessary for the control of the ISP conformational switch are illustrated in this cartoon rendition of the Q_P pocket. The PEWY motif and cd1 helix in gray represent a native (Resting) configuration. The ISPs in yellow and magenta are in oxidized and reduced forms, respectively. The heme b_L is red when it is reduced. The PEWY motif in blue stands for the open configuration as in the state with a bound Q_P site inhibitor. The cd1 helix in red symbolizes the conformation (On) as in the presence of a P_f inhibitor occupying the distal site (pink), and the cd1 helix in green shows the conformation (Off) when a P_m inhibitor is occupying the proximal site (purple). Cyt c₁ is shown in orange.

Figure 5. Structures of core proteins of bovine mitochondrial bc₁ complex

(A) Ribbon representation of the structure of the core-1 subunit showing two domains of the α-β structure related by an intradomain approximate twofold rotational axis perpendicular to the plane of the diagram (B) Structure of the core-2 in the form of a ribbon diagram showing in similar orientation as the core-1 subunit in (A). (C) Structure of core-1 (cyan) and core-2 (coral) heterodimer viewed parallel to the intersubunit approximate two-fold rotational axis. The two molecules are associated such that the N-terminal domain of core-1 is facing the C-terminal domain of core-2. The putative zinc-binding motif is shown as ball-and-stick models, which is detailed in (E). (D) Electrostatic potential surface representation of the core-1 and core-2 heterodimer. The surface is shown in the same orientation as in (C). Red surface represents negative potential and blue positive. (E) Structural arrangement of the zinc-binding motif in the core subunits of the bc₁ complex. Residues from the two α helices, αA (green) and αD (red) that are separated by more than 50 residues, contribute to the zinc-binding motif. Residues important for Zn binding from these two helices come together in the 3-D structure and are joined by ^BtR287 and ^BtK286 from the core-2 subunit (yellow). (F) Attachment of core proteins to the bc₁ complex. Core subunits are anchored to the TM region of the complex by recruiting and incorporating peptides from subunit 7 (red) and cyt c₁ (blue) into a β-sheet in the core-1 subunit. The ISP subunit (yellow) provides additional interactions with the core-1 subunit.

Figure 6. Structures of supernumerary subunits of the Btbc₁ complex in ribbon presentation

(A) Subunit 6, (B) subunit 7, (C) subunit 8, (D) subunit 9, (E) subunit 10, and (F) subunit 11.