Succinate dehydrogenase

Succinate dehydrogenase (SDH) or succinate-coenzyme Q reductase (SQR) or respiratory complex II is an enzyme complex, found in many bacterial cells and in the inner mitochondrial membrane of eukaryotes. It is the only enzyme that participates in both the citric acid cycle and oxidative phosphorylation. Histochemical analysis showing high succinate dehydrogenase in muscle demonstrates high mitochondrial content and high oxidative potential.

In step 6 of the citric acid cycle, SQR catalyzes the oxidation of succinate to fumarate with the reduction of ubiquinone to ubiquinol. This occurs in the inner mitochondrial membrane by coupling the two reactions together.

Structure

thumb|left | 300px | Image 5: Subunits of succinate dehydrogenase

Subunits

Mitochondrial and many bacterial SQRs are composed of four structurally different subunits: two hydrophilic and two hydrophobic. The first two subunits, a flavoprotein (SDHA) and an iron-sulfur protein (SDHB), form a hydrophilic head where enzymatic activity of the complex takes place. SDHA contains a covalently attached flavin adenine dinucleotide (FAD) cofactor and the succinate binding site and SDHB contains three iron-sulfur clusters: [2Fe-2S], [4Fe-4S], and [3Fe-4S]. The second two subunits are hydrophobic membrane anchor subunits, SDHC and SDHD. Human mitochondria contain two distinct isoforms of SDHA (Fp subunits type I and type II), these isoforms are also found in Ascaris suum and Caenorhabditis elegans. The subunits form a membrane-bound cytochrome b complex with six transmembrane helices containing one heme b group and a ubiquinone-binding site. Two phospholipid molecules, one cardiolipin and one phosphatidylethanolamine, are also found in the SDHC and SDHD subunits (not shown in the image). They serve to occupy the hydrophobic space below the heme b. These subunits are displayed in the attached image. SDHA is green, SDHB is teal, SDHC is fuchsia, and SDHD is yellow. Around SDHC and SDHD is a phospholipid membrane with the intermembrane space at the top of the image.

Table of subunit composition

{| border=1 class="wikitable" style="text-align:center"

!No.

!Subunit name

!Human protein

!Protein description from UniProt

!Pfam family with Human protein

| 1 || SDHA || SDHA_HUMAN || Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial || ,

| 2 || SDHB || SDHB_HUMAN || Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial || ,

| 3 || SDHC || C560_HUMAN || Succinate dehydrogenase cytochrome b560 subunit, mitochondrial ||

| 4 || SDHD || DHSD_HUMAN || Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial ||

Ubiquinone binding site

Two distinctive ubiquinone binding sites can be recognized on mammalian SDH – matrix-proximal QP and matrix-distal QD. Ubiquinone binding site Qp, which shows higher affinity to ubiquinone, is located in a gap composed of SDHB, SDHC, and SDHD. Ubiquinone is stabilized by the side chains of His207 of subunit B, Ser27 and Arg31 of subunit C, and Tyr83 of subunit D. The quinone ring is surrounded by Ile28 of subunit C and Pro160 of subunit B. These residues, along with Il209, Trp163, and Trp164 of subunit B, and Ser27 (C atom) of subunit C, form the hydrophobic environment of the quinone-binding pocket Qp. In contrast, ubiquinone binding site QD, which lies closer to inter-membrane space, is composed of SDHD only and has lower affinity to ubiquinone.

Succinate binding site

SDHA provides the binding site for the oxidation of succinate. The side chains Thr254, His354, and Arg399 of subunit A stabilize the molecule while FAD oxidizes and carries the electrons to the first of the iron-sulfur clusters, [2Fe-2S]. This can be seen in image 5.

Redox centers

The succinate-binding site and ubiquinone-binding site are connected by a chain of redox centers including FAD and the iron-sulfur clusters. This chain extends over 40 Å through the enzyme monomer. All edge-to-edge distances between the centers are less than the suggested 14 Å limit for physiological electron transfer. also called SDH5 in yeast and SDHE in bacteria) and by some of the Krebs cycle intermediates. Fumarate most strongly stimulates covalent flavinylation of SDHA. Through studies of the bacterial system, the mechanism of FAD attachment has been shown to involve a quinone:methide intermediate. In mitochondrial, but not bacterial, assembly, SDHA interacts with a second assembly factor called succinate dehydrogenase assembly factor 4 (SDHAF4; called SDH8 in yeast) before it is inserted into the final complex.

Proton transfer

To fully reduce the quinone in SQR, two electrons as well as two protons are needed. It has been argued that a water molecule (HOH39) arrives at the active site and is coordinated by His207 of subunit B, Arg31 of subunit C, and Asp82 of subunit D. The semiquinone species is protonated by protons delivered from HOH39, completing the ubiquinone reduction to ubiquinol. His207 and Asp82 most likely facilitate this process. Other studies claim that Tyr83 of subunit D is coordinated to a nearby histidine as well as the O1 carbonyl oxygen of ubiquinone. The histidine residue decreases the pKa of tyrosine, making it more suitable to donate its proton to the reduced ubiquinone intermediate.

Inhibitors

There are two distinct classes of inhibitors (SDHIs) of complex II: those that bind in the succinate pocket and those that bind in the ubiquinone pocket. Ubiquinone type inhibitors include carboxin and thenoyltrifluoroacetone. Succinate-analogue inhibitors include the synthetic compound malonate as well as the TCA cycle intermediates, malate and oxaloacetate. Indeed, oxaloacetate is one of the most potent inhibitors of Complex II. Why a common TCA cycle intermediate would inhibit Complex II is not entirely understood, though it may exert a protective role in minimizing reverse-electron transfer mediated production of superoxide by Complex I. Atpenin 5a are highly potent Complex II inhibitors mimicking ubiquinone binding.

Ubiquinone type inhibitors have been used as fungicides in agriculture since the 1960s. Carboxin was mainly used to control disease caused by basidiomycetes such as stem rusts and Rhizoctonia diseases. In the 1980s simple benzanilides were found to have comparable activity to carboxin and a number of these were marketed, including benodanil, flutolanil and mepronil. More recently, other compounds with a broader spectrum against a range of plant pathogens have been developed including boscalid, fluopyram, fluxapyroxad, pydiflumetofen and sedaxane. FRAC has a working group for SDHIs and recommends resistance management practices.

Complex II inhibitors are also used as insecticides and acaricides, in IRAC group 25.

Role in disease

The fundamental role of succinate-coenzyme Q reductase in both oxidative phosphorylation and the citric acid cycle makes it vital in all eukaryotic organisms. Loss of function of SDH via mutations or through toxins can cause a wide range of disease.

When SDH is dysfunctional in the citric acid cycle, it can lead to a buildup of the oncometabolite succinate, which can lead to tumorogenesis. This is well-known to occur in chromaffin cells, causing neuroendocrine tumors such as paraganglioma, renal carcinoma, and Gastrointestinal stromal tumor (GISTs). The penetrance data for SDH mutations causing tumorigenesis is lacking, and international guidelines suggest thorough screening for any carriers. The penetrance of paraganglioma in loss of function mutations of SDH is incomplete and varies by subunit. SDHB mutations have a penetrance between 8% and 37%, SDHD mutations have a penetrance between 38% and 64% with some maternal imprinting effects, and the penetrance for both SDHA and SDHC mutations are poorly studied, but likely between 1% and 30%. Mammalian SDH functions not only in energy generation, but also has a role in oxygen sensing. Buildup of succinate due to defective SDH can cause a pseudo-hypoxia and angiogenesis, both of which contribute to the distinctly vascular and characteristic "salt and pepper" appearance of paraganglioma on imaging.

Bi-Allelic loss of function mutations of SDHA, SDHB, SDHD, and SDHAF1 or monoallelic loss of function mutations of SDHA can cause Mitochondrial complex II deficiency. This disruption in oxidative phosphorylation can lead to Leigh syndrome, mitochondrial encephalopathy, optic atrophy, myopathy, and a spectrum of disease. These presentations can range from death within the first year of life or in utero to mild symptoms beginning as an adult.

Reduced levels SDH are observed post mortem in the brains of patients with Huntington's disease, and energy metabolism defects have been identified in both presymptomatic and symptomatic HD patients.

Since many viruses rely on the activity of the succinate dehydroginase as the complex II of the respiratory chain of human cells, blocking this enzyme using atpenin A5, inhibited SARS-CoV-2, dengue virus, respiratory syncytial virus, and influenza A virus with high selectivity indices in vitro.