3.D.10 The Prokaryotic Succinate Dehydrogenase (SDH) Family

The succinate oxidase and succinate:menaquinone reductase activities are lost when the transmembrane electrochemical proton potential (pmf) is abolished by rupture of the bacteria or addition of a protonophore. It had been proposed that the endergonic reduction of menaquinone by succinate is driven by the electrochemical proton potential. Opposite sides of the cytoplasmic membrane were envisaged to be separately involved in the binding of protons upon the reduction of menaquinone and their release upon succinate oxidation, with the two reactions linked by the transfer of two electrons through the enzyme. However, it has also been argued that the observed pmf dependence is not associated specifically with the succinate:menaquinone reductase.

Madej et al. (2006) described the purification, reconstitution into proteoliposomes, and functional characterization of the diheme-containing succinate:menaquinone reductase from B. licheniformis, and, with the help of the design, synthesis, and characterization of quinones with finely tuned oxidation/reduction potentials, provided evidence for the pmf-dependent catalysis of succinate oxidation by quinone as well as for pmf generation upon catalysis of fumarate reduction by quinol (see also Simon et al., 2008).

Membrane protein complexes can support both the generation and utilisation of a transmembrane electrochemical proton potential (Deltap), either by supporting transmembrane electron transfer coupled to protolytic reactions on opposite sides of the membrane or by supporting transmembrane proton transfer. The first mechanism has been demonstrated for the pmf-dependent catalysis of succinate oxidation by quinone in the case of the dihaem-containing succinate:menaquinone reductase (SQR) from the Gram-positive bacterium Bacillus licheniformis. This is physiologically relevant in that it allows the transmembrane potential to drive the endergonic oxidation of succinate by menaquinone by the dihaem-containing SQR of Gram-positive bacteria. A related but different respiratory membrane protein complex is the dihaem- containing quinol:fumarate reductase (QFR) of the ε-proteobacterium Wolinella succinogenes. For this enzyme, evidence has been obtained that both mechanisms are combined, so as to facilitate transmembrane electron transfer by proton transfer via an essential compensatory transmembrane proton transfer pathway ('E-pathway'). Although the reduction of fumarate by menaquinol is exergonic, it is not exergonic enough to support the generation of a pmf. This compensatory 'E-pathway' appears to be required by all dihaem-containing QFR enzymes and results in the overall reaction being electroneutral. However, Madej et al. 2009 showed that the reverse reaction, the oxidation of succinate by quinone, as catalysed by the W. succinogenes QFR, is electrogenic.

The di-heme family of succinate:quinone oxidoreductases support electron transfer across the biological membranes in which they are embedded (Lancaster 2013). In the case of the di-heme-containing succinate:menaquinone reductase (SQR) from Gram-positive bacteria and other menaquinone-containing bacteria, this results in an electrogenic reaction. This is physiologically relevant in that it allows the transmembrane electrochemical proton potential Δp to drive the endergonic oxidation of succinate by menaquinone. In the case of the reverse reaction, menaquinol oxidation by fumarate, catalysed by the di-heme-containing quinol:fumarate reductase (QFR), this electrogenic electron transfer reaction is compensated by proton transfer via an essential transmembrane proton transfer pathway ('E-pathway'). Although the reduction of fumarate by menaquinol is exergonic, it is not sufficiently exergonic to support the generation of a Δp. This compensatory 'E-pathway' appears to be required by all di-heme-containing QFR enzymes and results in the overall reaction being electroneutral (Lancaster 2013). Other members of this diverse family  and the crystal structure of the QFR from the anaerobic Wolinella succinogenes at 1.78Å resolution have been reviewed (Lancaster 2013). Interestingly, fumarate is a terminal electron acceptor in the mammalian electron transport chain (Spinelli et al. 2021).

The generalized reaction catalyzed by these bacterial SDHs may be:

succinate (in) + menaquinone (membrane) + 2H+ (out) ⇌ fumarate (in) + menaquinol (membrane) + 2H+ (in)



This family belongs to the Iron-Sulfur Protein (ISP) Superfamily.

 

References:

Gong, H., Y. Gao, X. Zhou, Y. Xiao, W. Wang, Y. Tang, S. Zhou, Y. Zhang, W. Ji, L. Yu, C. Tian, S.M. Lam, G. Shui, L.W. Guddat, L.L. Wong, Q. Wang, and Z. Rao. (2020). Cryo-EM structure of trimeric Mycobacterium smegmatis succinate dehydrogenase with a membrane-anchor SdhF. Nat Commun 11: 4245.

Guan, H.H., Y.C. Hsieh, P.J. Lin, Y.C. Huang, M. Yoshimura, L.Y. Chen, S.K. Chen, P. Chuankhayan, C.C. Lin, N.C. Chen, A. Nakagawa, S.I. Chan, and C.J. Chen. (2018). Structural insights into the electron/proton transfer pathways in the quinol:fumarate reductase from Desulfovibrio gigas. Sci Rep 8: 14935.

Hamann, N., E. Bill, J.E. Shokes, R.A. Scott, M. Bennati, and R. Hedderich. (2009). The CCG-domain-containing subunit SdhE of succinate:quinone oxidoreductase from Sulfolobus solfataricus P2 binds a [4Fe-4S] cluster. J Biol Inorg Chem 14: 457-470.

Lancaster, C.R. (2013). The di-heme family of respiratory complex II enzymes. Biochim. Biophys. Acta. 1827: 679-687.

Lancaster, C.R., E. Herzog, H.D. Juhnke, M.G. Madej, F.G. Müller, R. Paul, and P.G. Schleidt. (2008). Electroneutral and electrogenic catalysis by dihaem-containing succinate:quinone oxidoreductases. Biochem Soc Trans 36: 996-1000.

Madej, M.G., F.G. Müller, J. Ploch, and C.R. Lancaster. (2009). Limited reversibility of transmembrane proton transfer assisting transmembrane electron transfer in a dihaem-containing succinate:quinone oxidoreductase. Biochim. Biophys. Acta. 1787: 593-600.

Madej, M.G., H.R. Nasiri, N.S. Hilgendorff, H. Schwalbe, and C.R. Lancaster. (2006). Evidence for transmembrane proton transfer in a dihaem-containing membrane protein complex. EMBO. J. 25: 4963-4970.

Madej, M.G., H.R. Nasiri, N.S. Hilgendorff, H. Schwalbe, G. Unden, and C.R. Lancaster. (2006). Experimental evidence for proton motive force-dependent catalysis by the diheme-containing succinate:menaquinone oxidoreductase from the Gram-positive bacterium Bacillus licheniformis. Biochemistry 45: 15049-15055.

Simon, J., R.J. van Spanning, and D.J. Richardson. (2008). The organisation of proton motive and non-proton motive redox loops in prokaryotic respiratory systems. Biochim. Biophys. Acta. 1777: 1480-1490.

Spinelli, J.B., P.C. Rosen, H.G. Sprenger, A.M. Puszynska, J.L. Mann, J.M. Roessler, A.L. Cangelosi, A. Henne, K.J. Condon, T. Zhang, T. Kunchok, C.A. Lewis, N.S. Chandel, and D.M. Sabatini. (2021). Fumarate is a terminal electron acceptor in the mammalian electron transport chain. Science 374: 1227-1237.

Sun, F., X. Huo, Y. Zhai, A. Wang, J. Xu, D. Su, M. Bartlam, and Z. Rao. (2005). Crystal structure of mitochondrial respiratory membrane protein complex II. Cell 121: 1043-1057.

Xin, Y., Y.K. Lu, R. Fromme, P. Fromme, and R.E. Blankenship. (2009). Purification, characterization and crystallization of menaquinol:fumarate oxidoreductase from the green filamentous photosynthetic bacterium Chloroflexus aurantiacus. Biochim. Biophys. Acta. 1787: 86-96.

Zhou, X., Y. Gao, W. Wang, X. Yang, X. Yang, F. Liu, Y. Tang, S.M. Lam, G. Shui, L. Yu, C. Tian, L.W. Guddat, Q. Wang, Z. Rao, and H. Gong. (2021). Architecture of the mycobacterial succinate dehydrogenase with a membrane-embedded Rieske FeS cluster. Proc. Natl. Acad. Sci. USA 118:.

Examples:

TC#NameOrganismal TypeExample
3.D.10.1.1

Succinate:menaquinone oxidoreductase, SdhABC (pmf consuming when starting with succinate; pmf generating when starting with fumarate (the reverse reaction)).  Transmembrane electron transfer is coupled to protolytic reactions on opposite sides of the membrane, allowing the transmembrane pmf to drive the endergonic oxidation of succinate by menaquinone by the dihaem-containing SQR (Lancaster et al. 2008).

Bacteria

SdhABC of Bacillus licheniformis
SdhA (flavoprotein; 587aas) (Q65GF4)
SdhB (iron-sulfur center subunit; 254aas) (Q65GF5)
SdhC (transmembrane cytochrome c558 subunit; 202aas) (Q65GF3)

 
3.D.10.1.2

Succinate dehydrogenase/fumarate reductase, SdhABC.


Spirochaetes

Succinate dehydrogenase/fumarate reductase, SdhABC, of Leptospira interrogans

 
3.D.10.1.3

The diheme-containing quinol:fumarate reductase (QFR), FrdABC (Madej et al. 2009).  This enzyme complex is required for fumarate respiration using formate or sulfide as electron donor.  It mediates transmembrane electron transfer by proton transfer via a compensatory transmembrane proton transfer pathway ('E-pathway') (Lancaster et al. 2008). This is necessary because, although the reduction of fumarate by menaquinol is exergonic, it is not exergonic enough to support the generation of a pmf. This compensatory E-pathway appears to be required by all dihaem- containing QFR enzymes. The conservation of an essential acidic residue on transmembrane helix V (Glu-C180 in W. succinogenes QFR) provides a key for the sequence-based discrimination of these QFR enzymes from the dihaem-containing SQR enzymes (Lancaster et al. 2008). This enzyme complex may mediate transmembrane electron transfer coupled to protolytic reactions on opposite sides of the membrane and by transmembrane protontransport (Madej et al. 2006).

transfer.

Proteobacteria

FrdABC of Wolinella succinogenes (Vibrio succinogenes)

 
3.D.10.1.4

Succinate dehydrogenase, SdhABC, or type E succinate:quinone oxidoreductase (SQR) (Hamann et al. 2009).

Crenarchaeota

SDH of Sulfolobus tokodaii (S. sulfataricus)

 
3.D.10.1.5

Three subunit menaquinone:fumarate oxidoreductase (QfrABC or SdhABC ) (Xin et al. 2009).

Chlorobi

QfrABC of Chlorobium tepidum
QfrA, 646 aas (flavoprotein; FAD-containing)
QfrB, 257 aas (iron-sulfur protein)
QfrC, 240 aas and 5 TMSs (contains two b-type hemes and two menaquinones)

 
3.D.10.1.6

Succinate dehydrogenase complex, SdhABCD. 

SdhA, 598 aas and 1 TMS.  Flavoprotein subunit, X5H3P0.
SdhB, 257 aas and 1 TMS.  Iron-sulfur subunit, X5GWN5.
SdhC, 128 aas and 3 TMSs.  Cytochrome B556 subunit, X5H2Z3.
SdhD, 110 aas and 3 TMSs.  Membrane anchor subunit, X5HJ03

SdhABCD of Neorickettsia helminthoeca

 
3.D.10.1.7

Succinate dehydrogenase complex, or succinate:ubiquinone oxidoreductase (SQR) or  mitochondrial respiratory complex II of four subunits, SdhA, B, C and D.  Does not transport protons across the membrane, but all 4 subunits are homologous to the prokaryotic Sdh subunits that do transport protons.  It is an integral membrane protein complex in both the tricarboxylic acid cycle and aerobic respiration. Sun et al. 2005 reported the first crystal structure of Complex II from porcine heart at 2.4 Å resolution and its complex structure with inhibitors 3-nitropropionate and 2-thenoyltrifluoroacetone (TTFA) at 3.5 Å resolution. Complex II is comprised of two hydrophilic proteins, flavoprotein (Fp) and iron-sulfur protein (Ip), and two transmembrane proteins (CybL and CybS), as well as prosthetic groups required for electron transfer from succinate to ubiquinone. The structure correlates the protein environments around prosthetic groups with their unique midpoint redox potentials. Two ubiquinone binding sites are identified. The structure provides a bona fide model for study of the mitochondrial respiratory system and human mitochondrial diseases related to mutations in this complex (Sun et al. 2005).

Sdh complex of Homo sapiens

 
3.D.10.1.8

Quinol:fumarate reductase respiratory complex, FrdABC, where FrdA (627 aas) and FrdB (264 aas) are soluble proteins while FrdC has 218 aas and 5 TMSs.  The crystal structure has been determined at 3.6 Å resolution (Guan et al. 2018).  QFR in anaerobic bacteria catalyzes the reduction of fumarate to succinate by quinol in the anaerobic respiratory chain. The electron/proton-transfer pathway in the anaerobic sulphate-reducing bacterium Desulfovibrio gigas involves a homo-dimer, each protomer comprising two hydrophilic subunits, A and B, and one transmembrane subunit C, together with six redox cofactors including two b-hemes. One menaquinone molecule is bound near heme bL in the hydrophobic subunit C. This location of the menaquinone-binding site differs from the menaquinol-binding cavity proposed previously for QFR from Wolinella succinogenes (TC#3.D.10.1.3). The bound menaquinone may serve as an additional redox cofactor to mediate the proton-coupled electron transport across the membrane. Guan et al. 2018 proposed electron/proton-transfer pathways during the quinol-dependent reduction of fumarate to succinate in the D. gigas QFR.

QfrABC of Desulfovibrio gigas

 
3.D.10.1.9

Succinate dehydrogenase with 5 subunits, Sdh2, SdhABCDF. The cryo-EM structure of trimeric Mycobacterium smegmatis succinate dehydrogenase with a membrane-anchor, SdhF, has been determined (Gong et al. 2020).  Diheme-containing succinate:menaquinone oxidoreductases (Sdh) are widespread in Gram-positive bacteria. Gong et al. 2020 presented the 2.8 Å cryo-EM structure of Sdh, which forms a trimer with a membrane-anchored SdhF as a subunit of the complex (PDB 6LUM). The 3 kDa SdhF forms a single transmembrane helix, and this helix plays a role in blocking the canonically proximal quinone-binding site. The authors also identified two distal quinone-binding sites with bound quinones. One distal binding site is formed by neighboring subunits of the complex, and the electron/proton transfer pathway for succinate oxidation by menaquinone was revealed. The structure provides insight into the physiological significance of a trimeric respiratory complex II. The structure of the menaquinone binding site could provide a framework for the development of Sdh-selective anti-mycobacterial drugs (Gong et al. 2020). The architecture of SdhABC (type F), with a membrane-embedded Rieske FeS cluster, has been solved to 2.5 Å resolution (Zhou et al. 2021). A quinone-binding site and a rarely observed Rieske-type [2Fe-2S] cluster, the latter being embedded in the transmembrane region, were identified, and an electron transfer pathway that connects the substrate-binding and quinone-binding sites was identified (Zhou et al. 2021).

SdhABCDF of
Mycolicibacterium smegmatis (strain ATCC 700084) (Mycobacterium smegmatis)
SdhA, 584 aas, I7FYK4, flavoprotein subunit
SdhB, 261 aas, I7G4J1, iron-sulfur protein
SdhC, 144 aas and 3 TMSs, I7G657,
cytochrome B-556 subunit
SdhD, 156 aas and 3 TMSs, I7FGY0, hydrophobic membrane anchor protein
SdhF,  subunit of SDH, of 32 aas and one TMS, AWT56629.1