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614 a.a.
242 a.a.
140 a.a.
102 a.a.
 Succinate |
+ |
 ubiquinone |
= |
 fumarate |
+ |
 ubiquinol |
|---|
Bound ligand (Het Group name = FAD) corresponds exactly |
 Iron-sulfur |
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Key reference
DOI no: 10.1074/jbc.M511270200 J Biol Chem 281:5965-5972 (2006) PubMed id: 16371358
3-nitropropionic acid is a suicide inhibitor of mitochondrial respiration that, upon oxidation by complex II, forms a covalent adduct with a catalytic base arginine in the active site of the enzyme. L.S.Huang, G.Sun, D.Cobessi, A.C.Wang, J.T.Shen, E.Y.Tung, V.E.Anderson, E.A.Berry. ABSTRACT
We report three new structures of mitochondrial respiratory Complex II (succinate ubiquinone oxidoreductase, E.C. 1.3.5.1) at up to 2.1 A resolution, with various inhibitors. The structures define the conformation of the bound inhibitors and suggest the residues involved in substrate binding and catalysis at the dicarboxylate site. In particular they support the role of Arg(297) as a general base catalyst accepting a proton in the dehydrogenation of succinate. The dicarboxylate ligand in oxaloacetate-containing crystals appears to be the same as that reported for Shewanella flavocytochrome c treated with fumarate. The plant and fungal toxin 3-nitropropionic acid, an irreversible inactivator of succinate dehydrogenase, forms a covalent adduct with the side chain of Arg(297). The modification eliminates a trypsin cleavage site in the flavoprotein, and tandem mass spectroscopic analysis of the new fragment shows the mass of Arg(297) to be increased by 83 Da and to have the potential of losing 44 Da, consistent with decarboxylation, during fragmentation.
Selected figure(s)
Figure 1.
FIGURE 1. Overall structure of mitochondrial complex II. The stereo ribbon diagram is colored yellow and brown (flavoprotein), green (iron protein), pink (large anchor polypeptide, chain C), and blue (small anchor peptide, chain D). The CAP domain of the flavoprotein is colored brown. The green space-filling model at the intersection between the CAP domain and the rest of the flavoprotein is the malate-like ligand, and the extended blue ball-and-stick model starting just to the right of that is the FAD cofactor. Note the first helix of anchor peptide (Chain C) packs against a helix of the IP.Figure 4.
FIGURE 4. The dicarboxylate site in the 3-NP-treated enzyme. The density attributed to the ligand has shrunk and moved away from the flavin toward Arg^297 and His^253. It can be modeled by assuming two atoms from the backbone of 3-NP (C-3 and N) fuse with the guanidino group to form a five-membered ring, with loss of the two nitro oxygens. The carboxylate at the other end fits into the clearly forked density branching off the ring. 2F[o] - F[c] map contoured at 1.7.
The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2006, 281, 5965-5972) copyright 2006. Figures were selected by the author.
Author's comment These structures confirmed the role of Arg297 in ligand binding (and presumably catalysis) at the dicarboxylate active site. This had been suspected from mutagenesis and from the structure of homologous Flavocytochrome c of Shewanella, but had never been shown before in Complex II superfamily.
Structure 1YQ4 confirms the covalent binding of the plant and fungal toxin 3-nitropropionate, showing that the catalytic base arginine A297 is covalently modified. This is in contrast to a previous model from the lower-resolution structure of porcine complex II with nitropropionate bound.
-Edward Berry
Literature references that cite this PDB file's key reference
PubMed id Reference
19170876 H.D.Juhnke, H.Hiltscher, H.R.Nasiri, H.Schwalbe, and C.R.Lancaster (2009).
Production, characterization and determination of the real catalytic properties of the putative 'succinate dehydrogenase' from Wolinella succinogenes.Mol Microbiol, 71, 1088-1101.
19060309 K.Kawahara, T.Mogi, T.Q.Tanaka, M.Hata, H.Miyoshi, and K.Kita (2009).
Mitochondrial Dehydrogenases in the Aerobic Respiratory Chain of the Rodent Malaria Parasite Plasmodium yoelii yoelii.J Biochem, 145, 229-237.
19634179 N.Brunet, O.Tarabal, J.E.Esquerda, and J.Calderó (2009).
Excitotoxic motoneuron degeneration induced by glutamate receptor agonists and mitochondrial toxins in organotypic cultures of chick embryo spinal cord.J Comp Neurol, 516, 277-290.
19682208 R.Lagoa, C.Lopez-Sanchez, A.K.Samhan-Arias, C.M.Gañan, V.Garcia-Martinez, and C.Gutierrez-Merino (2009).
Kaempferol protects against rat striatal degeneration induced by 3-nitropropionic acid.J Neurochem, 111, 473-487.
19192292 R.M.Gawryluk, and M.W.Gray (2009).
A split and rearranged nuclear gene encoding the iron-sulfur subunit of mitochondrial succinate dehydrogenase in Euglenozoa.BMC Res Notes, 2, 16.
18418633 E.A.Berry, and F.A.Walker (2008).
Bis-histidine-coordinated hemes in four-helix bundles: how the geometry of the bundle controls the axial imidazole plane orientations in transmembrane cytochromes of mitochondrial complexes II and III and related proteins.J Biol Inorg Chem, 13, 481-498.
18296637 J.I.Yeh, U.Chinte, and S.Du (2008).
Structure of glycerol-3-phosphate dehydrogenase, an essential monotopic membrane enzyme involved in respiration and metabolism.Proc Natl Acad Sci U S A, 105, 3280-3285.
PDB codes: 2qcu 2r45 2r46 2r4e 2r4j
18536726 M.Jormakka, K.Yokoyama, T.Yano, M.Tamakoshi, S.Akimoto, T.Shimamura, P.Curmi, and S.Iwata (2008).
Molecular mechanism of energy conservation in polysulfide respiration.Nat Struct Mol Biol, 15, 730-737.
PDB codes: 2vpw 2vpx 2vpy 2vpz
18385138 T.M.Tomasiak, E.Maklashina, G.Cecchini, and T.M.Iverson (2008).
A threonine on the active site loop controls transition state formation in Escherichia coli respiratory complex II.J Biol Chem, 283, 15460-15468.
PDB code: 3cir
17376234 B.E.Baysal, E.C.Lawrence, and R.E.Ferrell (2007).
Sequence variation in human succinate dehydrogenase genes: evidence for long-term balancing selection on SDHA.BMC Biol, 5, 12.
17429617 K.Xiong, H.Cai, X.G.Luo, R.G.Struble, R.W.Clough, and X.X.Yan (2007).
Mitochondrial respiratory inhibition and oxidative stress elevate beta-secretase (BACE1) proteins and activity in vivo in the rat retina.Exp Brain Res, 181, 435-446.
17989224 Q.M.Tran, R.A.Rothery, E.Maklashina, G.Cecchini, and J.H.Weiner (2007).
Escherichia coli succinate dehydrogenase variant lacking the heme b.Proc Natl Acad Sci U S A, 104, 18007-18012.
18005427 S.L.Cole, and R.Vassar (2007).
The Alzheimer's disease beta-secretase enzyme, BACE1.Mol Neurodegener, 2, 22.
17050691 J.Zhang, F.E.Frerman, and J.J.Kim (2006).
Structure of electron transfer flavoprotein-ubiquinone oxidoreductase and electron transfer to the mitochondrial ubiquinone pool.Proc Natl Acad Sci U S A, 103, 16212-16217.
PDB codes: 2gmh 2gmj The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.
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