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PDBsum entry 1zp0
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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1zp0

 

 

 

 

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Contents
Protein chains
613 a.a. *
239 a.a. *
138 a.a. *
102 a.a. *
Ligands
FAD
3NP
FES
SF4
F3S
HEM
TTF ×2
Waters ×3
* Residue conservation analysis
PDB id:
1zp0
Name: Oxidoreductase
Title: Crystal structure of mitochondrial respiratory complex ii bound with 3-nitropropionate and 2-thenoyltrifluoroacetone
Structure: Fad-binding protein. Chain: a. Synonym: flavoprotein. Iron-sulfur protein. Chain: b. Large cytochrome binding protein. Chain: c. Small cytochrome binding protein. Chain: d
Source: Sus scrofa. Pig. Organism_taxid: 9823. Tissue: porcine heart. Tissue: porcine heart
Biol. unit: Tetramer (from PQS)
Resolution:
3.50Å     R-factor:   0.268     R-free:   0.293
Authors: F.Sun,X.Huo,Y.Zhai,A.Wang,J.Xu,D.Su,M.Bartlam,Z.Rao
Key ref:
F.Sun et al. (2005). Crystal structure of mitochondrial respiratory membrane protein complex II. Cell, 121, 1043-1057. PubMed id: 15989954 DOI: 10.1016/j.cell.2005.05.025
Date:
16-May-05     Release date:   12-Jul-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Q0QF01  (SDHA_PIG) -  Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial from Sus scrofa
Seq:
Struc: 		 
Seq:
Struc: 		664 a.a.
613 a.a.
Protein chain
Q007T0  (SDHB_PIG) -  Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial from Sus scrofa
Seq:
Struc: 		280 a.a.
239 a.a.
Protein chain
D0VWV4  (C560_PIG) -  Succinate dehydrogenase cytochrome b560 subunit, mitochondrial from Sus scrofa
Seq:
Struc: 		169 a.a.
138 a.a.
Protein chain
A5GZW8  (DHSD_PIG) -  Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial from Sus scrofa
Seq:
Struc: 		159 a.a.
102 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class 2: Chains A, B: E.C.1.1.5.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
   Enzyme class 3: Chains A, B: E.C.1.3.5.1  - succinate dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
      Reaction: a quinone + succinate = fumarate + a quinol
quinone
Bound ligand (Het Group name = TTF)
matches with 46.67% similarity 		+
succinate
Bound ligand (Het Group name = 3NP)
matches with 45.45% similarity 		= fumarate
 + quinol
      Cofactor: FAD; Iron-sulfur
FAD
Bound ligand (Het Group name = FAD) corresponds exactly 		Iron-sulfur
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1016/j.cell.2005.05.025 Cell 121:1043-1057 (2005)
PubMed id: 15989954  
 
 
Crystal structure of mitochondrial respiratory membrane protein complex II.
F.Sun, X.Huo, Y.Zhai, A.Wang, J.Xu, D.Su, M.Bartlam, Z.Rao.
 
  ABSTRACT  
 
The mitochondrial respiratory Complex II or succinate:ubiquinone oxidoreductase (SQR) is an integral membrane protein complex in both the tricarboxylic acid cycle and aerobic respiration. Here we report the first crystal structure of Complex II from porcine heart at 2.4 A resolution and its complex structure with inhibitors 3-nitropropionate and 2-thenoyltrifluoroacetone (TTFA) at 3.5 A 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 discussed and elucidated by TTFA binding. The Complex II structure provides a bona fide model for study of the mitochondrial respiratory system and human mitochondrial diseases related to mutations in this complex.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The Role of Complex II in the Mitochondrial Respiratory Chain 		Figure 5.
Figure 5. Ubiquinone Binding Sites
 
  The above figures are reprinted by permission from Cell Press: Cell (2005, 121, 1043-1057) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20706275 A.Lemarie, L.Huc, E.Pazarentzos, A.L.Mahul-Mellier, and S.Grimm (2011).
Specific disintegration of complex II succinate:ubiquinone oxidoreductase links pH changes to oxidative stress for apoptosis induction.
  Cell Death Differ, 18, 338-349.  
21406178 J.Chen, C.L.Chen, B.R.Alevriadou, J.L.Zweier, and Y.R.Chen (2011).
Excess no predisposes mitochondrial succinate-cytochrome c reductase to produce hydroxyl radical.
  Biochim Biophys Acta, 1807, 491-502.  
21402148 L.F.Dong, V.J.Jameson, D.Tilly, L.Prochazka, J.Rohlena, K.Valis, J.Truksa, R.Zobalova, E.Mahdavian, K.Kluckova, M.Stantic, J.Stursa, R.Freeman, P.K.Witting, E.Norberg, J.Goodwin, B.A.Salvatore, J.Novotna, J.Turanek, M.Ledvina, P.Hozak, B.Zhivotovsky, M.J.Coster, S.J.Ralph, R.A.Smith, and J.Neuzil (2011).
Mitochondrial targeting of α-tocopheryl succinate enhances its pro-apoptotic efficacy: A new paradigm for effective cancer therapy.
  Free Radic Biol Med, 50, 1546-1555.  
19802898 C.J.Ricketts, J.R.Forman, E.Rattenberry, N.Bradshaw, F.Lalloo, L.Izatt, T.R.Cole, R.Armstrong, V.K.Kumar, P.J.Morrison, A.B.Atkinson, F.Douglas, S.G.Ball, J.Cook, U.Srirangalingam, P.Killick, G.Kirby, S.Aylwin, E.R.Woodward, D.G.Evans, S.V.Hodgson, V.Murday, S.L.Chew, J.M.Connell, T.L.Blundell, F.Macdonald, and E.R.Maher (2010).
Tumor risks and genotype-phenotype-proteotype analysis in 358 patients with germline mutations in SDHB and SDHD.
  Hum Mutat, 31, 41-51.  
19739941 G.Lenaz, and M.L.Genova (2010).
Structure and organization of mitochondrial respiratory complexes: a new understanding of an old subject.
  Antioxid Redox Signal, 12, 961.  
20960097 H.Sato, G.Kanai, K.Hirabayshi, H.Kajiwara, J.Itoh, and R.Y.Osamura (2010).
L157X nonsense mutation of the succinate dehydrogenase subunit B gene in a Japanese patient with right paraaortic paraganglioma.
  Endocrine, 38, 18-23.  
19826804 K.McLuskey, A.W.Roszak, Y.Zhu, and N.W.Isaacs (2010).
Crystal structures of all-alpha type membrane proteins.
  Eur Biophys J, 39, 723-755.  
20667175 K.R.Vinothkumar, and R.Henderson (2010).
Structures of membrane proteins.
  Q Rev Biophys, 43, 65.  
20169582 L.Gille, K.Staniek, T.Rosenau, J.C.Duvigneau, and A.V.Kozlov (2010).
Tocopheryl quinones and mitochondria.
  Mol Nutr Food Res, 54, 601-615.  
20217235 L.Prochazka, L.F.Dong, K.Valis, R.Freeman, S.J.Ralph, J.Turanek, and J.Neuzil (2010).
alpha-Tocopheryl succinate causes mitochondrial permeabilization by preferential formation of Bak channels.
  Apoptosis, 15, 782-794.  
20484225 N.Burnichon, J.J.Brière, R.Libé, L.Vescovo, J.Rivière, F.Tissier, E.Jouanno, X.Jeunemaitre, P.Bénit, A.Tzagoloff, P.Rustin, J.Bertherat, J.Favier, and A.P.Gimenez-Roqueplo (2010).
SDHA is a tumor suppressor gene causing paraganglioma.
  Hum Mol Genet, 19, 3011-3020.  
20533897 P.R.Rich, and A.Maréchal (2010).
The mitochondrial respiratory chain.
  Essays Biochem, 47, 1.  
19924544 S.Huang, N.L.Taylor, R.Narsai, H.Eubel, J.Whelan, and A.H.Millar (2010).
Functional and composition differences between mitochondrial complex II in Arabidopsis and rice are correlated with the complex genetic history of the enzyme.
  Plant Mol Biol, 72, 331-342.  
20618733 Z.Cao, J.H.Song, Y.W.Kang, J.H.Yoon, S.W.Nam, J.Y.Lee, and W.S.Park (2010).
Analysis of succinate dehydrogenase subunit B gene alterations in gastric cancers.
  Pathol Int, 60, 559-565.  
19465911 D.Ghezzi, P.Goffrini, G.Uziel, R.Horvath, T.Klopstock, H.Lochmüller, P.D'Adamo, P.Gasparini, T.M.Strom, H.Prokisch, F.Invernizzi, I.Ferrero, and M.Zeviani (2009).
SDHAF1, encoding a LYR complex-II specific assembly factor, is mutated in SDH-defective infantile leukoencephalopathy.
  Nat Genet, 41, 654-656.  
19366681 D.L.Hoffman, and P.S.Brookes (2009).
Oxygen sensitivity of mitochondrial reactive oxygen species generation depends on metabolic conditions.
  J Biol Chem, 284, 16236-16245.  
20161522 H.B.Gray, and J.R.Winkler (2009).
Electron Flow through Proteins.
  Chem Phys Lett, 483, 1-9.  
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.  
19628817 H.X.Hao, O.Khalimonchuk, M.Schraders, N.Dephoure, J.P.Bayley, H.Kunst, P.Devilee, C.W.Cremers, J.D.Schiffman, B.G.Bentz, S.P.Gygi, D.R.Winge, H.Kremer, and J.Rutter (2009).
SDH5, a gene required for flavination of succinate dehydrogenase, is mutated in paraganglioma.
  Science, 325, 1139-1142.  
19949411 J.M.Shaw, and D.R.Winge (2009).
Shaping the mitochondrion: mitochondrial biogenesis, dynamics and dysfunction. Conference on Mitochondrial Assembly and Dynamics in Health and Disease.
  EMBO Rep, 10, 1301-1305.  
19122194 J.Morales, T.Mogi, S.Mineki, E.Takashima, R.Mineki, H.Hirawake, K.Sakamoto, S.Omura, and K.Kita (2009).
Novel Mitochondrial Complex II Isolated from Trypanosoma cruzi Is Composed of 12 Peptides Including a Heterodimeric Ip Subunit.
  J Biol Chem, 284, 7255-7263.  
19710024 J.Ruprecht, V.Yankovskaya, E.Maklashina, S.Iwata, and G.Cecchini (2009).
Structure of Escherichia coli succinate:quinone oxidoreductase with an occupied and empty quinone-binding site.
  J Biol Chem, 284, 29836-29846.
PDB codes: 2wdq 2wdr 2wdv
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.  
19492336 T.Huang, Y.Wan, Y.Zhu, X.Fang, N.Hiramatsu, K.Hayakawa, A.W.Paton, J.C.Paton, M.Kitamura, and J.Yao (2009).
Downregulation of gap junction expression and function by endoplasmic reticulum stress.
  J Cell Biochem, 107, 973-983.  
19505951 T.Mogi, T.Kawakami, H.Arai, Y.Igarashi, K.Matsushita, M.Mori, K.Shiomi, S.Omura, S.Harada, and K.Kita (2009).
Siccanin rediscovered as a species-selective succinate dehydrogenase inhibitor.
  J Biochem, 146, 383-387.  
19891782 Y.Liu, and D.R.Schubert (2009).
The specificity of neuroprotection by antioxidants.
  J Biomed Sci, 16, 98.  
19472180 Y.S.Zhang (2009).
The development of biochemistry and molecular biology in China.
  IUBMB Life, 61, 549-554.  
18682392 C.L.Chen, J.Chen, S.Rawale, S.Varadharaj, P.P.Kaumaya, J.L.Zweier, and Y.R.Chen (2008).
Protein tyrosine nitration of the flavin subunit is associated with oxidative modification of mitochondrial complex II in the post-ischemic myocardium.
  J Biol Chem, 283, 27991-28003.  
18363851 D.L.Denmark, and K.J.Buck (2008).
Molecular analyses and identification of promising candidate genes for loci on mouse chromosome 1 affecting alcohol physical dependence and associated withdrawal.
  Genes Brain Behav, 7, 599-608.  
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.  
18681855 E.López-Jiménez, J.M.de Campos, E.M.Kusak, I.Landa, S.Leskelä, C.Montero-Conde, L.J.Leandro-García, L.A.Vallejo, B.Madrigal, C.Rodríguez-Antona, M.Robledo, and A.Cascón (2008).
SDHC mutation in an elderly patient without familial antecedents.
  Clin Endocrinol (Oxf), 69, 906-910.  
18550551 G.Mustafa, Y.Ishikawa, K.Kobayashi, C.T.Migita, M.D.Elias, S.Nakamura, S.Tagawa, and M.Yamada (2008).
Amino acid residues interacting with both the bound quinone and coenzyme, pyrroloquinoline quinone, in Escherichia coli membrane-bound glucose dehydrogenase.
  J Biol Chem, 283, 22215-22221.  
18395845 H.O.Byun, H.Y.Kim, J.J.Lim, Y.H.Seo, and G.Yoon (2008).
Mitochondrial dysfunction by complex II inhibition delays overall cell cycle progression via reactive oxygen species production.
  J Cell Biochem, 104, 1747-1759.  
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
18372923 L.F.Dong, P.Low, J.C.Dyason, X.F.Wang, L.Prochazka, P.K.Witting, R.Freeman, E.Swettenham, K.Valis, J.Liu, R.Zobalova, J.Turanek, D.R.Spitz, F.E.Domann, I.E.Scheffler, S.J.Ralph, and J.Neuzil (2008).
Alpha-tocopheryl succinate induces apoptosis by targeting ubiquinone-binding sites in mitochondrial respiratory complex II.
  Oncogene, 27, 4324-4335.  
18843528 M.Hüttemann, I.Lee, A.Pecinova, P.Pecina, K.Przyklenk, and J.W.Doan (2008).
Regulation of oxidative phosphorylation, the mitochondrial membrane potential, and their role in human disease.
  J Bioenerg Biomembr, 40, 445-456.  
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
18347581 N.Sawada, J.Yao, N.Hiramatsu, K.Hayakawa, I.Araki, M.Takeda, and M.Kitamura (2008).
Involvement of hypoxia-triggered endoplasmic reticulum stress in outlet obstruction-induced apoptosis in the urinary bladder.
  Lab Invest, 88, 553-563.  
17967865 R.D.Guzy, B.Sharma, E.Bell, N.S.Chandel, and P.T.Schumacker (2008).
Loss of the SdhB, but Not the SdhA, subunit of complex II triggers reactive oxygen species-dependent hypoxia-inducible factor activation and tumorigenesis.
  Mol Cell Biol, 28, 718-731.  
18366324 R.Lill, and U.Mühlenhoff (2008).
Maturation of iron-sulfur proteins in eukaryotes: mechanisms, connected processes, and diseases.
  Annu Rev Biochem, 77, 669-700.  
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
18930525 Z.Chen (2008).
Biomedical science and technology in China.
  Lancet, 372, 1441-1443.  
17369262 A.M.James, M.S.Sharpley, A.R.Manas, F.E.Frerman, J.Hirst, R.A.Smith, and M.P.Murphy (2007).
Interaction of the mitochondria-targeted antioxidant MitoQ with phospholipid bilayers and ubiquinone oxidoreductases.
  J Biol Chem, 282, 14708-14718.  
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.  
17294131 J.Neuzil, J.C.Dyason, R.Freeman, L.F.Dong, L.Prochazka, X.F.Wang, I.Scheffler, and S.J.Ralph (2007).
Mitocans as anti-cancer agents targeting mitochondria: lessons from studies with vitamin E analogues, inhibitors of complex II.
  J Bioenerg Biomembr, 39, 65-72.  
18240421 M.Hüttemann, I.Lee, L.Samavati, H.Yu, and J.W.Doan (2007).
Regulation of mitochondrial oxidative phosphorylation through cell signaling.
  Biochim Biophys Acta, 1773, 1701-1720.  
17557793 N.Buzhynskyy, P.Sens, V.Prima, J.N.Sturgis, and S.Scheuring (2007).
Rows of ATP synthase dimers in native mitochondrial inner membranes.
  Biophys J, 93, 2870-2876.  
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.  
17636259 S.S.Szeto, S.N.Reinke, B.D.Sykes, and B.D.Lemire (2007).
Ubiquinone-binding site mutations in the Saccharomyces cerevisiae succinate dehydrogenase generate superoxide and lead to the accumulation of succinate.
  J Biol Chem, 282, 27518-27526.  
17480203 X.Huo, D.Su, A.Wang, Y.Zhai, J.Xu, X.Li, M.Bartlam, F.Sun, and Z.Rao (2007).
Preliminary molecular characterization and crystallization of mitochondrial respiratory complex II from porcine heart.
  FEBS J, 274, 1524-1529.  
17848555 Y.R.Chen, C.L.Chen, D.R.Pfeiffer, and J.L.Zweier (2007).
Mitochondrial complex II in the post-ischemic heart: oxidative injury and the role of protein S-glutathionylation.
  J Biol Chem, 282, 32640-32654.  
17327211 Z.Rao (2007).
History of protein crystallography in China.
  Philos Trans R Soc Lond B Biol Sci, 362, 1035-1042.  
17011837 A.Bacsi, M.Woodberry, W.Widger, J.Papaconstantinou, S.Mitra, J.W.Peterson, and I.Boldogh (2006).
Localization of superoxide anion production to mitochondrial electron transport chain in 3-NPA-treated cells.
  Mitochondrion, 6, 235-244.  
17056719 D.W.Walker, P.Hájek, J.Muffat, D.Knoepfle, S.Cornelison, G.Attardi, and S.Benzer (2006).
Hypersensitivity to oxygen and shortened lifespan in a Drosophila mitochondrial complex II mutant.
  Proc Natl Acad Sci U S A, 103, 16382-16387.  
16484232 E.Maklashina, T.M.Iverson, Y.Sher, V.Kotlyar, J.Andréll, O.Mirza, J.M.Hudson, F.A.Armstrong, R.A.Rothery, J.H.Weiner, and G.Cecchini (2006).
Fumarate reductase and succinate oxidase activity of Escherichia coli complex II homologs are perturbed differently by mutation of the flavin binding domain.
  J Biol Chem, 281, 11357-11365.
PDB code: 2b76
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
16920246 K.A.Foster, F.Galeffi, F.J.Gerich, D.A.Turner, and M.Müller (2006).
Optical and pharmacological tools to investigate the role of mitochondria during oxidative stress and neurodegeneration.
  Prog Neurobiol, 79, 136-171.  
16371358 L.S.Huang, G.Sun, D.Cobessi, A.C.Wang, J.T.Shen, E.Y.Tung, V.E.Anderson, and E.A.Berry (2006).
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.
  J Biol Chem, 281, 5965-5972.
PDB codes: 1yq3 1yq4 2fbw
16935256 L.S.Huang, J.T.Shen, A.C.Wang, and E.A.Berry (2006).
Crystallographic studies of the binding of ligands to the dicarboxylate site of Complex II, and the identity of the ligand in the "oxaloacetate-inhibited" state.
  Biochim Biophys Acta, 1757, 1073-1083.
PDB codes: 2h88 2h89
16950775 Q.M.Tran, R.A.Rothery, E.Maklashina, G.Cecchini, and J.H.Weiner (2006).
The quinone binding site in Escherichia coli succinate dehydrogenase is required for electron transfer to the heme b.
  J Biol Chem, 281, 32310-32317.  
16407191 R.Horsefield, V.Yankovskaya, G.Sexton, W.Whittingham, K.Shiomi, S.Omura, B.Byrne, G.Cecchini, and S.Iwata (2006).
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, 281, 7309-7316.
PDB codes: 2acz 2ad0
16808843 R.Paddenberg, P.König, P.Faulhammer, A.Goldenberg, U.Pfeil, and W.Kummer (2006).
Hypoxic vasoconstriction of partial muscular intra-acinar pulmonary arteries in murine precision cut lung slices.
  Respir Res, 7, 93.  
16085649 R.F.Anderson, R.Hille, S.S.Shinde, and G.Cecchini (2005).
Electron transfer within complex II. Succinate:ubiquinone oxidoreductase of Escherichia coli.
  J Biol Chem, 280, 33331-33337.  
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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