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1.3.5.1: succinate dehydrogenase

This is an abbreviated version!
For detailed information about succinate dehydrogenase, go to the full flat file.

Word Map on EC 1.3.5.1

Reaction

succinate
+
a quinone
=
fumarate
 +
a quinol

Synonyms

8-methylmenaquinol:fumarate reductase, AaSdhB, bacterial succinate:quinone oxidoreductase flavoprotein, complex II, Complex II homolog, complex II of the respiratory chain, complex II succinate:ubiquinone oxidoreductase, DCPIP oxidoreductase, dehydrogenase, succinate, dehydrogenase/complex II, EC 1.3.5.4, EC 1.3.99.1, Fcc3, fdrB, FL cyt, Flavocytochrome c3, FRD, FrdA, FRdABCD, FrdC, FRdCAB, FrdD, fumarate reductase, fumarate reductase complex, fumaric hydrogenase, Ifc3, Iron(III)-induced flavocytochrome C3, iron-sulfur subunit of succinate dehydrogenase, menaquinol-1 fumarate reductase, menaquinol-fumarate oxidoreductase, menaquinol:fumarate oxidoreductase, methylmenaquinol:fumarate reductase, MFR, MFR complex, MfrA, MfrB, mitochondrial complex II, mitochondrial succinate dehydrogenase, mitochondrial succinate:ubiquinone oxidoreductase, More, mQFR, MSMEG_0416, MSMEG_0417, MSMEG_0418, MSMEG_0419, MSMEG_0420, MSMEG_1669, MSMEG_1670, MSMEG_1671, MSMEG_1672, non-classical succinate:quinone reductase, QFR, quinol-fumarate reductase, quinol:fumarate reductase, SDG, SDG-1, SDG-2, SDH, SDH1, SDH2, SDH2-1, SDH2-2, SDH3, SDH4, SdhA, sdhABE, SDHB, SdhC, sdhCAB, SdhCDAB, SdhD, SDISP, SQR, succinate dehydrogenase, succinate dehydrogenase (caldariellaquinone), succinate dehydrogenase (quinone), succinate dehydrogenase B, succinate dehydrogenase complex, succinate dehydrogenase flavoprotein subunit Sdh1p, succinate dehydrogenase iron-sulfur protein, succinate dehydrogenase iron-sulphur protein, succinate dehydrogenase subunit B, succinate oxidoreductase, succinate-2,6-dichlorophenolindophenol oxidoreductase, succinate-coenzyme Q reductase, succinate-quinone oxidoreductase, succinate-quinone reductase, succinate-ubiquinone oxidoreductase, succinate:caldariellaquinone oxidoreductase, succinate:menaquinone 7-reductase, succinate:menaquinone oxidoreductase, succinate:menaquinone reductase, succinate:MK reductase, succinate:quinone oxidoreductase, succinate:quinone reductase, succinate:quinone reductases, succinate:ubiquinone oxidoreductase, succinate:ubiquinone reductase, succinic acid dehydrogenase, succinic dehydrogenase, succinodehydrogenase, succinyl dehydrogenase, Tneu_0423

ECTree

     1 Oxidoreductases
         1.3 Acting on the CH-CH group of donors
             1.3.5 With a quinone or related compound as acceptor
                1.3.5.1 succinate dehydrogenase

Crystallization

Crystallization on EC 1.3.5.1 - succinate dehydrogenase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified native enzyme by dialysis method using a reservoir solution containing 15% w/v PEG 3350, 100 mM Tris-HCl, pH 8.4, 200 mM NaCl, 1 mM sodium malonate or fumarate, 0.06% w/v n-dodecyl ethylene glycol monoether C12E8, and 0.04% w/v n-dodecyl-bet-D-maltoside, 2-3 days, X-ray diffraction structure determination and analysis at 2.81-2.91 A resolution, molecular replacement
structure of subunits, binding sites, structure of complex II, pathway of electron transfer
-
X-ray diffraction data up to 3.2 Å resolution
-
by the hanging-drop vapour-diffusion technique
-
crystal structure of QFR to 3.3 A resolution. Enzyme contains two quinone species, presumably menaquinol, bound to the transmembrane-spanning region. The binding sites for the two quinone molecules are termed QP and QD, indicating their positions proximal, QP, or distal, QD, to the site of fumarate reduction in the hydrophilic flavoprotein and iron-sulfur protein subunits. Co-crystallization studies of the Escherichia coli QFR with the quinol-binding site inhibitors 2-heptyl-4-hydroxyquinoline-N-oxide and 2-[1-(p-chlorophenyl)ethyl] 4,6-dinitrophenol establish that both inhibitors block the binding of MQH2 at the QP site. In the structures with the inhibitor bound at QP, no density is observed at QD. The conserved acidic residue, Glu29 in subunit FrdC, in the Escherichia coli enzyme may act as a proton shuttle from the quinol during enzyme turnover
crystallization conditions are screened for succinate-quinone oxidoreductase that is solubilized and purified using 2.5% (w/v) sucrose monolaurate and 0.5% (w/v) Lubrol PX, respectively, and two different crystal forms are obtained in the presence of detergent mixtures composed of n-alkyl-oligoethylene glycol monoether and n-alkyl-maltoside. Crystallization takes place before detergent phase separation occurrs and the type of detergent mixture affects the crystal form
-
fumarate reductase, determined at 3.3 A, belongs to the type D enzymes: contains two hydrophobic subunits and no heme group
-
hanging drop vapor diffusion method, x-ray structure of mutant E49Q
hanging-drop vapour-diffusion method, the enzyme is cocrystallized with the ubiquinone binding-site inhibitor Atpenin A5 (AA5) to confirm the binding position of the inhibitor and reveal additional structural details of the Q-site
-
hanging-drop vapour-diffusion, SQR in 20 mM Tris-HCl, pH 7.6, 0.05% THESIT is mixed with an equal volume of reservoir solution containing 100 mM Na-HEPES, pH 7.5, 200 mM, CaCl2 and 28% polyethylene glycol 400, crystals diffract to 2.6 A resolution
-
PDB code: 1FUM, structure of the QFR monomer, with the covalently bound FAD cofactor, showing the iron-sulfur clusters [4Fe-4S], [3Fe-3S], and [2Fe-2S] and the two menaquinone molecules
purified enzyme QFR alone r with bound FLiG in two crystal forms, one grown from the lipidic cubic phase and one grown from dodecyl maltoside micelles, the first exhibiting crystal packing similar to previous crystal forms, while the latter displays a unique crystal packing providing the view of the QFR active site without a dicarboxylate ligand. For LCP crystallization 25 mg/ml protein (QFR or QFR-FliG) is mixed in a 40:60 ratio with 1-(9Z-octadecenoyl)-rac-glycerol (9.9 MAG), crystals are grown using 50 nl mesophase and 800 nl precipitant containing 200 mM NH4F, 100 mM Bis-Tris pH 7.5, 22% PEG 400, and 5% pentaerythritol propoxylate, crystals of QFR grow using the same conditions as crystals of QFR-FliG, with the crystals from the QFR-FliG mixture being better suited to diffraction analysis. For micellar crystallization of QFR-FliG in 20 mM Tris pH 7.4, 0.02% DDM, sitting drop vapor diffusion method is used, mixing of with 200 nl of 25 mg/ml protein and 200 nl of reservoir solution, containing 10-20% PEG 400-900, 15-50 mM divalent cation (CaCl2, Ca(CH3COO)2, or MgCl2), and 50 mM Bis-Tris, pH 6.5, X-ray diffraction structure determination and analysis at 7.5 and 3.35 A resolution, respectively
purified FrdA mutant E245Q, hanging-drop vapor diffusion method, mixing of 0.001 ml of 15 mg/ml protein in 25 mM Tris-HCl, pH 7.4, 1 mM EDTA, 0.02% C12E9, with 0.001 ml of reservoir solution containing 275mM sodium malonate, 19% PEG 6000, 100 mM sodium citrate, pH 4.0, 1 mM EDTA, and 0.001% dithiothreitol, and equilibration against 1 ml of reservoir solution, 20°C, X-ray diffraction structure determination and analysis at 4.25 A resolution
purified SdhA in complex with SdhE, hanging-drop vapor diffusion, mixing of 0.001 ml of 6.3 mg/ml protein in 50 mM Tris-HCl, pH 8.0, 300 mM NaCl with 0.001 ml of crystallization solution containing 0.1 M HEPES, pH 7.5, 0.2 M MgCl2 hexahydrate, 30% w/v PEG 3350, and 40 mM NaF, at 20°C, X-ray diffraction structure determination and analysis at 2.15 A resolution
structure of SQR at 2.6 A resolution
structure of SQR is reported at 2.6 A resolution. The SQR redox centers are arranged in a manner that aids the prevention of reactive oxygen species formation at the flavin adenine dinucleotide. This is likely to be the main reason SQR is expressed during aerobic respiration rather than the related enzyme fumarate reductase, which produces high levels of reactive oxygen species
structure of subunits, binding sites, structure of complex II, pathway of electron transfer
-
subunit FrdC mutant E29L, to 2.95 A resolution. The sequential removal of the two menaquinol protons may be accompanied by a rotation of the naphthoquinone ring to optimize the interaction with a second proton shuttling pathway
three new structures of Escherichia coli succinate-quinone oxidoreductase are solved. One with the specific quinone-binding site (Q-site) inhibitor carboxin present is solved at 2.4 A resolution and reveals how carboxin inhibits the Q-site. The other new structures are with the Q-site inhibitor pentachlorophenol and with an empty Q-site. Comparison of the new succinate-quinone oxidoreductase structures shows how subtle rearrangements of the quinone-binding site accommodate the different inhibitors. The position of conserved water molecules near the quinone binding pocket leads to a reassessment of possible water-mediated proton uptake networks that complete reduction of ubiquinone
-
sitting-drop vapour diffusion method. the crystals have the potential to diffract at least 2.0 A with optimization of post-crystal-growth treatment and cryoprotection. The most common form of crystals is the space group P2(1)2(1)2(1) with approximate unit-cell parameters a = 70 A, b = 84 A, c = 290 A. On a few occasions using slightly different conditions a second form has been obtained with space group P2(1) and unit cell parameters a = 120 A, b = 201 A, c = 68 A, alpha = beta = gamma = 90°
-
structure of complex II in presence of oxaloacetate or with the endogenous inhibitor bound, structure of the malonate-bound complex
-
purified native enzyme, hanging drop vapour diffusion method, mixing of 0.001 ml of protein solution and 0.001 ml of reservoir solution, and equilibration against 0.15 ml of reservoir solution containing 100 mM NaCl, 28% PEG 4000, and 100 mM Tris, pH 8.5, at 18 °C for two weeks, X-ray diffraction structure determination and analysis at resolution 3.6 A, molecular replacement method using the structure of QFR from Wolinella succinogenes (PDB ID 2BS2) without redox cofactors as the search model, modelling
Megalodesulfovibrio gigas
hanging drop method, crystal structure of complex II from porcine heart at 2.4 A resolution and its complex structure with inhibitors 3-nitropropionate and 2-thenoyltrifluoroacetone at 3.5 A resolution
-
molecular docking, molecular dynamics simulation, and molecular mechanics/Poisson-Boltzmann surface area calculations for complexes with carboxamide inhibitors. The acid moiety of carboxamide fungicides inserts into the ubiquinone binding site of SQR, forming van der Waals interactions with subunit C residues R46, S42, and subunit B residues I218, and P169, while the amine moiety extends to the mouth of the Q-site, forming van der Waals interactions with subunit C residues W35, I43, and I30. The carbonyl oxygen atom of the carboxamide forms hydrogen bonds with subunit B W173 and subunit DY91
-
partially purified enzyme, crystal growth in ammonium sulfate preparation precipitate, X-ray diffraction structure determination and analysis at 2.4 A resolution
-
fumarate reductase, refined at 2.2-A resolution, belongs to the type B enzymes: contains one hydrophobic subunit and two heme groups
-
structure of subunits, binding sites, structure of complex II, pathway of electron transfer
-
the structure of the enzyme is determined at 2.2 A resolution by X-ray crystallography
-