Succinate Dehydrogenase

From Proteopedia

spinqualitylabelsall models Succinate dehydrogenase containing flavoprotein subunit (Sdha) (grey), iron-sulfur subunit (Sdhb) (green), cytochrome B560 subunit (Sdhc) (pink) and cytochrome B small subunit (Sdhd) (yellow), FAD, Fe2S2, Fe4S4 and Fe3S4 complex with protoporphyrin, malonate, benzamide derivative and α-phosphatidyl-β-oleoyl-γ-palmitoyl-phosphatidylethanolamine, 3ae1 Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image Succinate Dehydrogenase (PDB = 2wdv with empty ubiquinone binding site; PDB = 1nek with ubiquinone bound), also called succinate-coenzyme Q reductase (SQR) or Complex II, is a tetrameric enzyme found in the cell membrane of some bacteria and the inner mitochondrial membrane of mammalian cells. It is classified as an α+β protein, as it contains of α helices and antiparallel β sheets. It is involved in two aspects of digestion; it catalyzes the oxidation of succinate to fumarate in the citric acid cycle by simultaneously reducing ubiquinone to ubiquinol in the electron transport chain [1]. Contents 1 Structure 2 Binding sites 2.1 Succinate 2.2 Ubiquinone Structure The tetramer is composed of . The hydrophilic subunits are named SdhA (PDB = 2wdq) and SdhB; the former is a flavoprotein containing a covalently-bound FAD cofactor and a binding site for succinate, while the latter is a Fe-S protein bearing the three iron-sulfur clusters 2Fe-2S, 3Fe-4S, and 4Fe-4S. The hydrophobic subunits, termed SdhC and SdhD, anchor the protein in the mitochondrial membrane and formally comprise cytochrome b [2] [3]. This cytochrome contains six transmembrane α-helices, a heme b group, and a binding site for ubiquinone located in a space bounded by SdhB, SdhC, and SdhD [3] [4]. Binding sites Succinate The binding site for succinate, in which the stereospecific dehydrogenation of succinate to fumarate is catalyzed, is located entirely on SdhA. stabilize the substrate with hydrogen bonding, while FAD removes the electrons and carries them to the first iron-sulfur cluster, 2Fe-2S, of SdhB [5]. During this transfer, FAD is reduced to FADH2 [6]. The Km for this reaction is approximately 10E(-3), while the Vmax is approximately 100 nmol/min/mg of protein [7]. Ubiquinone The binding site for ubiquinone, in which the substrate is reduced to ubiquinol, is bordered by subunits B, C, and D. Residues His207 of SdhB, Ser27 and Arg31 of SdhC, and Tyr83 of SdhD stabilize ubiquinone, while residues Pro160, Trp163, Trp164, and Ile209 of SdhB and Ser27 and Ile28 of SdhC provide the necessary hydrophobic environment that stabilizes the ring [4]. In the associated figure from PDB 1nek, the as follows: orange indicates the FAD cofactor, green shows the Fe-S clusters, cyan indicates ubiquinone in its binding site, yellow shows Ca2+ ions, navy blue indicates oxaloacetate, pink is cardiolipin, brown is ephrin, and the heme group is indicated by the lime green structure. The exact function of some of these ligands with regard to succinate dehydrogenase remains unclear; ephrin, for example is suspected to be involved in certain cell signaling pathways in animal development [8].

Mechanisms

Succinate oxidation

The exact mechanism for the oxidation of succinate to fumarate has not yet been elucidated. The initial deprotonation may be performed by FAD, Glu255, Arg286, or His242 of SdhA, and the following elimination may be a concerted E2 or E1cb elimination. In the concerted mechanism, the α-carbon is deprotonated by a base as FAD removes a hydride from the β-carbon; this is shown in image 1 ^[9].

Image 1: Oxidation of succinate to fumarate through E2 elimination (from Adamandalex in Wikimedia Commons http://en.wikipedia.org/wiki/File:S.D.Oxidation_of_Succinate_E2.gif).

In the proposed E1cb mechanism, the deprotonation leads to the formation of an enolate intermediate; FAD then removes the hydride, as shown in Image 2 ^[9].

Image 2: Oxidation of succinate to fumarate via E1cb elimination (from Adamandalex in Wikimedia Commons http://en.wikipedia.org/wiki/File:S.D.Oxidation_of_Succinate_E1cb.gif).

Ubiquinone reduction

Ubiquinone is initially oriented in the active site such that the O1 carbonyl group interacts with Tyr83 of SdhD via hydrogen bonding. The electrons removed during the oxidation reaction are conveyed through the iron-sulfur clusters to 3Fe-4S; their presence on that cluster stimulates the substrate to reorient so that a second hydrogen bond between the of SdhC may form. The electrons are transferred to the substrate individually, with the addition of the first producing a radical semiquinone and the second completing the reduction to ubiquinol. This mechanism is illustrated in image 3 ^[9].

Image 3: Reduction of ubiquinone to ubiquinol (from Adamandalex in Wikimedia Commons http://en.wikipedia.org/wiki/File:QuinoneMechanism.gif).

Regulation

Since succinate dehydrogenase possesses multiple active sites that catalyze two different reactions, two classes of inhibitors function on the enzyme. The first class, which includes succinate analogs--both naturally-occuring TCA cycle intermediates like malate and oxaloacetate and the synthetic analog, malonate--contains some of the strongest succinate dehydrogenase inhibitors. The second class of inhibitors, which includes the ubiquinone analogs thenoyltrifluoroacetone and carboxin, binds to the ubiquinone active site and prevents reduction of the substrate^[10].

3D structures of succinate dehydrogenase

Updated on 24-September-2014

SDH

2wdv - EcSDH flavoprotein + Fe-S protein + cytochrome B-556 + membrane anchor protein subunits – Escherichia coli
2wp9 - EcSDH flavoprotein + Fe-S protein (mutant) + cytochrome B-556 + membrane anchor protein subunits
2ws3, 2wu2, 2wu5 - EcSDH flavoprotein + Fe-S protein + cytochrome B-556 + membrane anchor protein subunits (mutant)
3aef, 1zoy - pSDH flavoprotein + Fe-S protein + cytochrome B subunits - pig
3vra, 3vr8 - prSDH flavoprotein + Fe-S protein + cytochrome B subunits – pig roundworm
2h88 - cSDH flavoprotein + IP + cytochrome B subunits - chicken
2lm4 – SDH assembly factor subunit – yeast – NMR

SDH binary complexes

1nek – EcSDH flavoprotein + Fe-S protein + cytochrome B-556 + membrane anchor protein subunits + ubiquinone
1nen - EcSDH flavoprotein + Fe-S protein + cytochrome B-556 + membrane anchor protein subunits + dinitrophenol-17
2acz - EcSDH flavoprotein + Fe-S protein + cytochrome B-556 + membrane anchor protein subunits + atpenin
2wdq - EcSDH flavoprotein + Fe-S protein + cytochrome B-556 + membrane anchor protein subunits + carboxin
2wdr - EcSDH flavoprotein + Fe-S protein + cytochrome B-556 + membrane anchor protein subunits + pentachlorophenol
3abv, 3ae1, 3ae2, 3ae3, 3ae4, 3ae5, 3ae6, 3ae7, 3ae8, 3ae9, 3aea, 3aeb, 3aec, 3aed, 3aeg - pSDH flavoprotein + Fe-S protein + cytochrome B subunits + benzamide derivative
3aee - pSDH flavoprotein + Fe-S protein + cytochrome B subunits + atpenin
2fbw, 2wqy - cSDH flavoprotein + IP + cytochrome B subunits + carboxin
2h89 - cSDH flavoprotein + IP + cytochrome B subunits + malonate
3vr9 - prSDH flavoprotein + Fe-S protein + cytochrome B subunits + flutolanil

SDH ternary complexes

3sfd - pSDH flavoprotein + Fe-S protein + cytochrome B subunits + oxalacetate + pentachlorophenol
3sfe - pSDH flavoprotein + Fe-S protein + cytochrome B subunits + oxalacetate + thiabendazole
1zp0 - pSDH flavoprotein + Fe-S protein + cytochrome B subunits + thenoyltrifluoroactone + nitropropionate
1yq3 - cSDH flavoprotein + IP + cytochrome B subunits + ubiquinone + oxalacetate
1yq4 - cSDH flavoprotein + IP + cytochrome B subunits + ubiquinone + nitropropionate
3vrb - prSDH flavoprotein + Fe-S protein + cytochrome B subunits + flutolanil + fumarate

References

1. ↑ Oyedotun KS, Lemire BD. The quaternary structure of the Saccharomyces cerevisiae succinate dehydrogenase. Homology modeling, cofactor docking, and molecular dynamics simulation studies. J Biol Chem. 2004 Mar 5;279(10):9424-31. Epub 2003 Dec 12. PMID:14672929 doi:10.1074/jbc.M311876200
2. ↑ Tomitsuka E, Hirawake H, Goto Y, Taniwaki M, Harada S, Kita K. Direct evidence for two distinct forms of the flavoprotein subunit of human mitochondrial complex II (succinate-ubiquinone reductase). J Biochem. 2003 Aug;134(2):191-5. PMID:12966066
3. ↑ ^{3.0 3.1} Yankovskaya V, Horsefield R, Tornroth S, Luna-Chavez C, Miyoshi H, Leger C, Byrne B, Cecchini G, Iwata S. Architecture of succinate dehydrogenase and reactive oxygen species generation. Science. 2003 Jan 31;299(5607):700-4. PMID:12560550 doi:10.1126/science.1079605
4. ↑ ^{4.0 4.1} Horsefield R, Yankovskaya V, Sexton G, Whittingham W, Shiomi K, Omura S, Byrne B, Cecchini G, Iwata S. Structural and computational analysis of the quinone-binding site of complex II (succinate-ubiquinone oxidoreductase): a mechanism of electron transfer and proton conduction during ubiquinone reduction. J Biol Chem. 2006 Mar 17;281(11):7309-16. Epub 2005 Dec 27. PMID:16407191 doi:http://dx.doi.org/10.1074/jbc.M508173200
5. ↑ Kenney WC. The reaction of N-ethylmaleimide at the active site of succinate dehydrogenase. J Biol Chem. 1975 Apr 25;250(8):3089-94. PMID:235539
6. ↑ Voet, Donald, Charlotte W. Pratt, and Judith G. Voet. Fundamentals of Biochemistry: Life at the Molecular Level. 2nd Ed. Hoboken, NJ: Wiley, 2008.
7. ↑ Vinogradov AD, Kotlyar AB, Burov VI, Belikova YO. Regulation of succinate dehydrogenase and tautomerization of oxaloacetate. Adv Enzyme Regul. 1989;28:271-80. PMID:2624174
8. ↑ Boyd AW, Lackmann M. Signals from Eph and ephrin proteins: a developmental tool kit. Sci STKE. 2001 Dec 11;2001(112):re20. PMID:11741094 doi:10.1126/stke.2001.112.re20
9. ↑ ^{9.0 9.1 9.2} Tran QM, Rothery RA, Maklashina E, Cecchini G, Weiner JH. The quinone binding site in Escherichia coli succinate dehydrogenase is required for electron transfer to the heme b. J Biol Chem. 2006 Oct 27;281(43):32310-7. Epub 2006 Sep 1. PMID:16950775 doi:10.1074/jbc.M607476200
10. ↑ Muller FL, Liu Y, Abdul-Ghani MA, Lustgarten MS, Bhattacharya A, Jang YC, Van Remmen H. High rates of superoxide production in skeletal-muscle mitochondria respiring on both complex I- and complex II-linked substrates. Biochem J. 2008 Jan 15;409(2):491-9. PMID:17916065 doi:10.1042/BJ20071162