TCDB is operated by the Saier Lab Bioinformatics Group
TCIDNameDomainKingdom/PhylumProtein(s)
3.D.3.1.1









Ubiquinol:cytochrome c oxidoreductase
Bacteria
Proteobacteria
Cytochrome bc1 complex of Paracoccus denitrificans
3.D.3.1.2









Proton pumping cytochrome bc1 complex of 3 dissimilar subunits, PetABC.  The pathway of transmembrane electron transfer has been determined and compared with that of the B6f complex from the same organism which is strikingly different (Bhaduri et al. 2017).

Bacteria
Proteobacteria
Cytochrome bc1 Complex of Rhodobacter capsulatus
Cytochrome b, PetB, of 437 aas and 10 TMSs in a 5 + 5 TMS arrangement (P0CY47)
Cytochrome c1, PetA, of 279 aas and 2 TMSs, N- and C-terminal (D5ANZ4)
Iron-sulfur subunit of 191 aas and 1 TMS (P0CY48)
3.D.3.2.1









Ubiquinol:cytochrome c oxidoreductase

Eukaryota
Metazoa
Cytochrome bc1 complex of Bos taurus
3.D.3.2.2









Proton-translocating cytochrome bc1/Rieske complex. Trophozoites of P. falciparum are inhibited by inhibitors such as atovaquone, buparvaquone and decoquinate (Meier et al. 2018).

Eukaryota
Apicomplexa
Cytbc1 complex of Plasmodium falciparum
Cytb of 376 aas and 9 TMSs
cytc1 of 394 aas and 2 TMSsd
Rieske of 355 aas and 1 or 2 TMSs
3.D.3.3.1









Ubiquinol:cytochrome c oxidoreductase.  The cytochrome bc1 complex resides in the inner membrane of mitochondria and transfers electrons from ubiquinol to cytochrome c. This electron transfer is coupled to the translocation of protons across the membrane by the protonmotive Q cycle mechanism. This mechanism topographically separates reduction of quinone and reoxidation of quinol at sites on opposite sites of the membrane, referred to as the center N (Qn site) and the center P (Qp site), respectively. Both are located on cytochrome b, a transmembrane protein of the bc1 complex that is encoded on the mitochondrial genome (Ding et al. 2006).

Eukaryota
Fungi
Cytochrome bc1 complex of Saccharomyces cerevisiae
3.D.3.4.1









Menaquinone:cytochrome c oxidoreductase
Bacteria
Firmicutes
Cytochrome bc1 complex of Bacillus subtilis
3.D.3.5.1









Plastoquinol:plastocyanine reductase
Bacteria
Cyanobacteria
Cytochrome b6f complex of Synechocystis PCC6803
3.D.3.5.2









Cytochrome b6f complex, PetB, PetC, PetD, PetM, Hcf164. The dimeric photosynthetic cytochrome b6f complex, a 16-mer of eight distinct subunits and 26 transmembrane helices, catalyzes transmembrane proton-coupled electron transfer for energy storage. Using a 2.5 Å crystal structure of the dimeric complex, Hasan and Cramer 2014 identified 23 distinct lipid-binding sites per monomer. Annular lipids provide a connection for super-complex formation with the photosystem-I reaction center and the LHCII kinase for transmembrane signaling. Internal lipids mediate crosslinking to stabilize the domain-swapped iron-sulfur protein subunit, dielectric heterogeneity within intermonomer and intramonomer electron transfer pathways, and dimer stabilization through lipid-mediated intermonomer interactions.  In the cytochrome b6f complex with the quinol analog, stigmatellin, which partitions in the Qp portal of the bc1 complex, but not of b6f, the Qp portal is partially occluded in the b6f complex relative to bc1. Occlusion of the Qp portal is attributed to the presence of the chlorophyll phytyl tail, which increases the quinone residence time within the Qp portal and is inferred to be a cause of enhanced superoxide production (Hasan et al. 2014).  PetD subunit integration into the thylakoid membrane is a post-translational and an SRP-dependent process that requires the formation of a cpSRP-cpFtsY-ALB3-PetD complex (Króliczewski et al. 2017). The b6f complex plays a role in trans-membrane signal transduction from reductant. The effect of the p-side of the electron transport chain on the regulation of light energy to the two photosystems by trans-side phosphorylation of the light-harvesting chlorophyll protein has been discussed (Cramer 2018). The cryo-EM structure of the spinach cytochrome b6 f complex has been solved at 3.6 A resolution (Malone et al. 2019). The cytb6f complex links electron transfer between photosystems I and II and converting solar energy into a pmf for ATP synthesis. Electron transfer within cytb6 f occurs via the quinol (Q) cycle, which catalyses the oxidation of plastoquinol (PQH2) and the reduction of both plastocyanin (PC) and plastoquinone (PQ) at two separate sites via electron bifurcation. In higher plants, cytb6 f also acts as a redox-sensing hub, pivotal to the regulation of light harvesting and cyclic electron transfer that protect against metabolic and environmental stresses. Malone et al. 2019 presented a 3.6 Å resolution cryo-EM structure of the dimeric cytb6 f complex from spinach, which reveals the structural basis for operation of the Q cycle and its redox-sensing function. The complex contains up to three natively bound PQ molecules. The first, PQ1, is located in one cytb6 f monomer near the PQ oxidation site (Qp), adjacent to haem bp and chlorophyll a. Two conformations of the chlorophyll a phytyl tail were resolved, one that prevents access to the Qp site and another that permits it, supporting a gating function for the chlorophyll a involved in redox sensing. PQ2 straddles the intermonomer cavity, partially obstructing the PQ reduction site (Qn) on the PQ1 side and committing the electron transfer network to turnover at the occupied Qn site in the neighbouring monomer. A conformational switch involving the haem cn propionate promotes two-electron, two-proton reduction at the Qn site and avoids formation of the reactive intermediate semiquinone. The location of a tentatively assigned third PQ molecule is consistent with a transition between the Qp and Qn sites in opposite monomers during the Q cycle. The spinach cytb6 f structure therefore provides new insights into how the complex fulfils its catalytic and regulatory roles in photosynthesis (Malone et al. 2019). Cytochrome b6f (cytb6f) lies at the heart of the light-dependent reactions of oxygenic photosynthesis, where it serves as a link between photosystem II (PSII) and photosystem I (PSI) through the oxidation and reduction of the electron carriers plastoquinol (PQH2) and plastocyanin (Pc). A mechanism of electron bifurcation, known as the Q-cycle, couples electron transfer to the generation of a transmembrane proton gradient for ATP synthesis. Cytb6f catalyses the rate-limiting step in linear electron transfer, is pivotal for cyclic electron transfer and plays a key role as a redox-sensing hub involved in the regulation of light-harvesting, electron transfer and photosynthetic gene expression (Malone et al. 2021).  Xiao et al. 2022 investigated the phytotoxicity of reduced graphene oxide (RGO), graphene oxide (GO) and amine-functionalized graphene (G-NH2) on Brassica napus L. RGO impaired photosynthesis mainly by decreasing the chlorophyll content and Rubisco activity. This effect of RGO could be due to its toxicity on sulfate transmembrane transporter and nitrogen metabolism, which ultimately led to nutrient imbalance. However, GO directly damaged the photosystem by disrupting the chloroplast structure, and a decrease in Rubisco activity indicated that GO also inhibits carbon fixation. Gene-level analysis demonstrated that GO has toxicity on the chloroplast membrane, photosystem, photosynthethic electron transport and F-type ATPase (Xiao et al. 2022). Regulation of the generation of reactive oxygen species during photosynthetic electron transport has been discussed (Krieger-Liszkay and Shimakawa 2022). Cyclic electron transfer and photoreduction of oxygen contribute to the size of the proton gradient. The yield of singlet oxygen production in photosystem II is regulated by changes in the midpoint potential of its primary quinone acceptor. In addition, numerous antioxidants inside the photosystems, the antenna and the thylakoid membrane quench or scavenge ROS (Krieger-Liszkay and Shimakawa 2022).

Eukaryota
Viridiplantae
Cytochrome b6f complex of Arabidopsis thaliana
3.D.3.5.3









Cytochrome b6/f complex, PetABCD of (cyt f; cyt b6, iron sulfur protein, and subunit 4, respectively, of 324, 215, 179, and 160 aas, respectively (Soo et al. 2017).

Bacteria
Cyanobacteria
PetABCD of Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2)
3.D.3.5.4









The three component QcrABC cytochrome bc1 (bcc) complex.  The bc1 complex catalyzes the oxidation of menaquinol and the reduction of a cytochrome c in the respiratory chain. The bc1 complex operates through a Q-cycle mechanism that couples electron transfer to generation of the proton gradient that drives ATP synthesis. QcrA is an iron-sulfur (2Fe-2S) protein of 353 aas and 3 central TMSs; QcrB is a cytochrom b protein that contains two quinone binding sites, one for oxidations, and one for reduction of 545 aas and 9 TMSs, while  QcrC is a membrane-bound diheme c-type cytochrome with 269 aas and 2 TMSs, one N-terminal, and one C-terminal.  QcrABC forms a complex with CtaCDEF (TC# 3.D.4.4.5), a cytochrome aa3 oxidase complex (Falke et al. 2018). This supercomplex is required for spore-specific nitrate reductase 1 activity (Falke et al. 2019).

Bacteria
Actinobacteria
QcrABC of Streptomyces coelicolor
3.D.3.5.5









The Ubiquinol-cytochrome oxidase supercomplex with 8 subunits. In the mycobacterial electron-transport chain, respiratory complex III passes electrons from menaquinol to complex IV, which in turn reduces oxygen, the terminal acceptor. Electron transfer is coupled to transmembrane proton translocation. Wiseman et al. 2018 isolated, biochemically characterized, and determined the structure of the obligate III2IV2 supercomplex from Mycobacterium smegmatis. The supercomplex has quinol:O2 oxidoreductase activity without exogenous cytochrome c and includes a superoxide dismutase subunit that may detoxify reactive oxygen species produced during respiration. Menaquinone is bound in both the Qo and Qi sites of complex III. The complex III-intrinsic diheme cytochrome cc subunit, which functionally replaces both cytochrome c1 and soluble cytochrome c in canonical electron-transport chains, displays two conformations: one in which it provides a direct electronic link to complex IV and another in which it serves as an electrical switch interrupting the connection (Wiseman et al. 2018).

Bacteria
Actinobacteria
The III2/IV2 supercomplex of Mycobacterium smegmatis
3.D.3.5.6









Cytochrome b6f complex of 10 subunits, PetA, B, C1-3, D, E, G, J, L, M and N. It transports H+ and electrons across the membrane. Lipids contribute to the stability and activity of the enzyme complex (Bhaduri et al. 2019).

Bacteria
Cyanobacteria
Cyt b6f of Nostoc sp. PCC7120
PetA, 333 aas
PetB, 215 aas
PetC3 = PetC4, 178 aas
PetD, 160 aas
PetE, 139 aas
PetG, 37 aas
PetJ, 111 aas
PetL, 31 aas
PetM, 34 aas
PetN, 29 aas
PetC1, 179 aas
PetC2, 178 aa
3.D.3.5.7









Cytochrome b6f complex including 11 subunits, A - K.  CryoEM structures are known (Proctor et al. 2022).

Bacteria
Terrabacteria group
Cytochrome b6f complex including 8 subunits, A - H.
7R0W_A, 222 aas and 5 TMSs
7R0W_B, 160 aas and 3 TMSs
7R0W_C, 328 aas and 2 TMSs, N- and C-terminal
7R0W_D, 192 aas and 1 N-terminal TMS
7R0W_E, 32 aas and 1 TMS
7R0W_F, 36 aas and 1 TMS
7R0W_G, 38 aas and 1 TMS
7R0W_H, 29 aas and 1 TM