1qjd Citations

Structural and mechanistic mapping of a unique fumarate reductase.

Nat Struct Biol 6 1108-12 (1999)
Cited: 81 times
EuropePMC logo PMID: 10581550

Abstract

The 1.8 A resolution crystal structure of the tetraheme flavocytochrome c3, Fcc3, provides the first mechanistic insight into respiratory fumarate reductases or succinate dehydrogenases. The multi-redox center, three-domain protein shows a 40 A long 'molecular wire' allowing rapid conduction of electrons through a new type of cytochrome domain onto the active site flavin, driving the reduction of fumarate to succinate. In this structure a malate-like molecule is trapped in the enzyme active site. The interactions between this molecule and the enzyme suggest a clear mechanism for fumarate reduction in which the substrate is polarized and twisted, facilitating hydride transfer from the reduced flavin and subsequent proton transfer. The enzyme active site in the oxidized form is completely buried at the interface between the flavin-binding and the clamp domains. Movement of the cytochrome and clamp domains is postulated to allow release of the product.

Reviews - 1qjd mentioned but not cited (2)

  1. Multi-haem cytochromes in Shewanella oneidensis MR-1: structures, functions and opportunities. Breuer M, Rosso KM, Blumberger J, Butt JN. J R Soc Interface 12 20141117 (2015)
  2. Direct Electron Transfer of Enzymes Facilitated by Cytochromes. Ma S, Ludwig R. ChemElectroChem 6 958-975 (2019)

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  1. 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. Huang LS, Sun G, Cobessi D, Wang AC, Shen JT, Tung EY, Anderson VE, Berry EA. J. Biol. Chem. 281 5965-5972 (2006)
  2. Structure of Escherichia coli succinate:quinone oxidoreductase with an occupied and empty quinone-binding site. Ruprecht J, Yankovskaya V, Maklashina E, Iwata S, Cecchini G. J. Biol. Chem. 284 29836-29846 (2009)
  3. 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. Huang LS, Shen JT, Wang AC, Berry EA. Biochim. Biophys. Acta 1757 1073-1083 (2006)
  4. Comparative void-volume analysis of psychrophilic and mesophilic enzymes: Structural bioinformatics of psychrophilic enzymes reveals sources of core flexibility. Paredes DI, Watters K, Pitman DJ, Bystroff C, Dordick JS. BMC Struct Biol 11 42 (2011)
  5. Electronic coupling between heme electron-transfer centers and its decay with distance depends strongly on relative orientation. Smith DM, Rosso KM, Dupuis M, Valiev M, Straatsma TP. J Phys Chem B 110 15582-15588 (2006)
  6. PANDORA: keyword-based analysis of protein sets by integration of annotation sources. Kaplan N, Vaaknin A, Linial M. Nucleic Acids Res 31 5617-5626 (2003)
  7. Structure prediction of domain insertion proteins from structures of individual domains. Berrondo M, Ostermeier M, Gray JJ. Structure 16 513-527 (2008)
  8. Geometric restraint drives on- and off-pathway catalysis by the Escherichia coli menaquinol:fumarate reductase. Tomasiak TM, Archuleta TL, Andréll J, Luna-Chávez C, Davis TA, Sarwar M, Ham AJ, McDonald WH, Yankovskaya V, Stern HA, Johnston JN, Maklashina E, Cecchini G, Iverson TM. J. Biol. Chem. 286 3047-3056 (2011)
  9. Crystallographic investigation of the ubiquinone binding site of respiratory Complex II and its inhibitors. Huang LS, Lümmen P, Berry EA. Biochim Biophys Acta Proteins Proteom 1869 140679 (2021)
  10. A Novel, NADH-Dependent Acrylate Reductase in Vibrio harveyi. Bertsova YV, Serebryakova MV, Baykov AA, Bogachev AV. Appl Environ Microbiol 88 e0051922 (2022)
  11. Biodegradation of pollutants by exoelectrogenic bacteria is not always performed extracellularly. Jeuken LJC. Environ Microbiol 24 1835-1837 (2022)
  12. Imidazole and nitroimidazole derivatives as NADH-fumarate reductase inhibitors: Density functional theory studies, homology modeling, and molecular docking. Campos-Fernández L, Ortiz-Muñiz R, Cortés-Barberena E, Mares-Sámano S, Garduño-Juárez R, Soriano-Correa C. J Comput Chem 43 1573-1595 (2022)
  13. Interdomain Linker of the Bioelecrocatalyst Cellobiose Dehydrogenase Governs the Electron Transfer. Zhang L, Laurent CVFP, Schwaiger L, Wang L, Ma S, Ludwig R. ACS Catal 13 8195-8205 (2023)
  14. Molecular basis of maintaining an oxidizing environment under anaerobiosis by soluble fumarate reductase. Kim S, Kim CM, Son YJ, Choi JY, Siegenthaler RK, Lee Y, Jang TH, Song J, Kang H, Kaiser CA, Park HH. Nat Commun 9 4867 (2018)


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  1. Bacterial respiration: a flexible process for a changing environment. Richardson DJ. Microbiology (Reading, Engl.) 146 ( Pt 3) 551-571 (2000)
  2. P450 BM3: the very model of a modern flavocytochrome. Munro AW, Leys DG, McLean KJ, Marshall KR, Ost TW, Daff S, Miles CS, Chapman SK, Lysek DA, Moser CC, Page CC, Dutton PL. Trends Biochem. Sci. 27 250-257 (2002)
  3. Function and structure of complex II of the respiratory chain. Cecchini G. Annu. Rev. Biochem. 72 77-109 (2003)
  4. The 'porin-cytochrome' model for microbe-to-mineral electron transfer. Richardson DJ, Butt JN, Fredrickson JK, Zachara JM, Shi L, Edwards MJ, White G, Baiden N, Gates AJ, Marritt SJ, Clarke TA. Mol. Microbiol. 85 201-212 (2012)
  5. Progress in understanding structure-function relationships in respiratory chain complex II. Ackrell BA. FEBS Lett. 466 1-5 (2000)
  6. Still a puzzle: why is haem covalently attached in c-type cytochromes? Barker PD, Ferguson SJ. Structure 7 R281-90 (1999)
  7. Cytopathies involving mitochondrial complex II. Ackrell BA. Mol. Aspects Med. 23 369-384 (2002)
  8. Succinate: quinone oxidoreductases: new insights from X-ray crystal structures. Lancaster CR, Kröger A. Biochim. Biophys. Acta 1459 422-431 (2000)
  9. Intermediary metabolism in protists: a sequence-based view of facultative anaerobic metabolism in evolutionarily diverse eukaryotes. Ginger ML, Fritz-Laylin LK, Fulton C, Cande WZ, Dawson SC. Protist 161 642-671 (2010)
  10. Multi-heme proteins: nature's electronic multi-purpose tool. Bewley KD, Ellis KE, Firer-Sherwood MA, Elliott SJ. Biochim. Biophys. Acta 1827 938-948 (2013)
  11. Analyzing your complexes: structure of the quinol-fumarate reductase respiratory complex. Iverson TM, Luna-Chavez C, Schröder I, Cecchini G, Rees DC. Curr. Opin. Struct. Biol. 10 448-455 (2000)
  12. Flavin-containing heme enzymes. Mowat CG, Gazur B, Campbell LP, Chapman SK. Arch. Biochem. Biophys. 493 37-52 (2010)
  13. Catalysis in fumarate reductase. Reid GA, Miles CS, Moysey RK, Pankhurst KL, Chapman SK. Biochim. Biophys. Acta 1459 310-315 (2000)
  14. Molecular details of multielectron transfer: the case of multiheme cytochromes from metal respiring organisms. Paquete CM, Louro RO. Dalton Trans 39 4259-4266 (2010)
  15. Catalytic mechanisms of complex II enzymes: a structural perspective. Iverson TM. Biochim. Biophys. Acta 1827 648-657 (2013)
  16. Diversity of parasite complex II. Harada S, Inaoka DK, Ohmori J, Kita K. Biochim. Biophys. Acta 1827 658-667 (2013)
  17. Defining a direction: electron transfer and catalysis in Escherichia coli complex II enzymes. Maklashina E, Cecchini G, Dikanov SA. Biochim. Biophys. Acta 1827 668-678 (2013)
  18. Structures of redox enzymes. Munro AW, Taylor P, Walkinshaw MD. Curr. Opin. Biotechnol. 11 369-376 (2000)
  19. Extracellular reduction of solid electron acceptors by Shewanella oneidensis. Beblawy S, Bursac T, Paquete C, Louro R, Clarke TA, Gescher J. Mol. Microbiol. 109 571-583 (2018)
  20. Electron transfer in natural and unnatural flavoporphyrins. Singh R, Geetanjali, Chauhan SM. Bioorg. Chem. 32 140-169 (2004)
  21. Incorporation of respiratory cytochromes in liposomes: an efficient strategy to study the respiratory chain. Nantes IL, Mugnol KC. J Liposome Res 18 175-194 (2008)
  22. An evolving view of complex II-noncanonical complexes, megacomplexes, respiration, signaling, and beyond. Iverson TM, Singh PK, Cecchini G. J Biol Chem 299 104761 (2023)

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  1. Identification of 42 possible cytochrome C genes in the Shewanella oneidensis genome and characterization of six soluble cytochromes. Meyer TE, Tsapin AI, Vandenberghe I, de Smet L, Frishman D, Nealson KH, Cusanovich MA, van Beeumen JJ. OMICS 8 57-77 (2004)
  2. Structure of electron transfer flavoprotein-ubiquinone oxidoreductase and electron transfer to the mitochondrial ubiquinone pool. Zhang J, Frerman FE, Kim JJ. Proc. Natl. Acad. Sci. U.S.A. 103 16212-16217 (2006)
  3. A structurally conserved water molecule in Rossmann dinucleotide-binding domains. Bottoms CA, Smith PE, Tanner JJ. Protein Sci. 11 2125-2137 (2002)
  4. Structure of glycerol-3-phosphate dehydrogenase, an essential monotopic membrane enzyme involved in respiration and metabolism. Yeh JI, Chinte U, Du S. Proc. Natl. Acad. Sci. U.S.A. 105 3280-3285 (2008)
  5. Identification and characterization of a novel cytochrome c(3) from Shewanella frigidimarina that is involved in Fe(III) respiration. Gordon EH, Pike AD, Hill AE, Cuthbertson PM, Chapman SK, Reid GA. Biochem. J. 349 153-158 (2000)
  6. Genetic characterization of a single bifunctional enzyme for fumarate reduction and succinate oxidation in Geobacter sulfurreducens and engineering of fumarate reduction in Geobacter metallireducens. Butler JE, Glaven RH, Esteve-Núñez A, Núñez C, Shelobolina ES, Bond DR, Lovley DR. J. Bacteriol. 188 450-455 (2006)
  7. Crystal structures at atomic resolution reveal the novel concept of "electron-harvesting" as a role for the small tetraheme cytochrome c. Leys D, Meyer TE, Tsapin AS, Nealson KH, Cusanovich MA, Van Beeumen JJ. J. Biol. Chem. 277 35703-35711 (2002)
  8. Crystal structures of two aromatic hydroxylases involved in the early tailoring steps of angucycline biosynthesis. Koskiniemi H, Metsä-Ketelä M, Dobritzsch D, Kallio P, Korhonen H, Mäntsälä P, Schneider G, Niemi J. J. Mol. Biol. 372 633-648 (2007)
  9. Redox Linked Flavin Sites in Extracellular Decaheme Proteins Involved in Microbe-Mineral Electron Transfer. Edwards MJ, White GF, Norman M, Tome-Fernandez A, Ainsworth E, Shi L, Fredrickson JK, Zachara JM, Butt JN, Richardson DJ, Clarke TA. Sci Rep 5 11677 (2015)
  10. The 1.3-Angstrom-resolution crystal structure of beta-ketoacyl-acyl carrier protein synthase II from Streptococcus pneumoniae. Price AC, Rock CO, White SW. J. Bacteriol. 185 4136-4143 (2003)
  11. Identification of a small tetraheme cytochrome c and a flavocytochrome c as two of the principal soluble cytochromes c in Shewanella oneidensis strain MR1. Tsapin AI, Vandenberghe I, Nealson KH, Scott JH, Meyer TE, Cusanovich MA, Harada E, Kaizu T, Akutsu H, Leys D, Van Beeumen JJ. Appl. Environ. Microbiol. 67 3236-3244 (2001)
  12. Multi-heme cytochromes--new structures, new chemistry. Mowat CG, Chapman SK. Dalton Trans 3381-3389 (2005)
  13. A third crystal form of Wolinella succinogenes quinol:fumarate reductase reveals domain closure at the site of fumarate reduction. Lancaster CR, Gross R, Simon J. Eur. J. Biochem. 268 1820-1827 (2001)
  14. Solution-based structural analysis of the decaheme cytochrome, MtrA, by small-angle X-ray scattering and analytical ultracentrifugation. Firer-Sherwood MA, Ando N, Drennan CL, Elliott SJ. J Phys Chem B 115 11208-11214 (2011)
  15. A proton delivery pathway in the soluble fumarate reductase from Shewanella frigidimarina. Pankhurst KL, Mowat CG, Rothery EL, Hudson JM, Jones AK, Miles CS, Walkinshaw MD, Armstrong FA, Reid GA, Chapman SK. J Biol Chem 281 20589-20597 (2006)
  16. Regulation of nitrite resistance of the cytochrome cbb3 oxidase by cytochrome c ScyA in Shewanella oneidensis. Yin J, Jin M, Zhang H, Ju L, Zhang L, Gao H. Microbiologyopen 4 84-99 (2015)
  17. NO reductase activity of the tetraheme cytochrome C554 of Nitrosomonas europaea. Upadhyay AK, Hooper AB, Hendrich MP. J. Am. Chem. Soc. 128 4330-4337 (2006)
  18. A threonine on the active site loop controls transition state formation in Escherichia coli respiratory complex II. Tomasiak TM, Maklashina E, Cecchini G, Iverson TM. J. Biol. Chem. 283 15460-15468 (2008)
  19. Proton delivery to ferryl heme in a heme peroxidase: enzymatic use of the Grotthuss mechanism. Efimov I, Badyal SK, Metcalfe CL, Macdonald I, Gumiero A, Raven EL, Moody PC. J. Am. Chem. Soc. 133 15376-15383 (2011)
  20. Production, characterization and determination of the real catalytic properties of the putative 'succinate dehydrogenase' from Wolinella succinogenes. Juhnke HD, Hiltscher H, Nasiri HR, Schwalbe H, Lancaster CR. Mol. Microbiol. 71 1088-1101 (2009)
  21. Characterization of transcriptional regulation of Shewanella frigidimarina Fe(III)-induced flavocytochrome c reveals a novel iron-responsive gene regulation system. Reyes-Ramirez F, Dobbin P, Sawers G, Richardson DJ. J. Bacteriol. 185 4564-4571 (2003)
  22. NMR structure of the haem core of a novel tetrahaem cytochrome isolated from Shewanella frigidimarina: identification of the haem-specific axial ligands and order of oxidation. Pessanha M, Brennan L, Xavier AV, Cuthbertson PM, Reid GA, Chapman SK, Turner DL, Salgueiro CA. FEBS Lett. 489 8-13 (2001)
  23. Thermodynamic characterization of a tetrahaem cytochrome isolated from a facultative aerobic bacterium, Shewanella frigidimarina: a putative redox model for flavocytochrome c3. Pessanha M, Louro RO, Correia IJ, Rothery EL, Pankhurst KL, Reid GA, Chapman SK, Turner DL, Salgueiro CA. Biochem. J. 370 489-495 (2003)
  24. Analysis of covalent flavinylation using thermostable succinate dehydrogenase from Thermus thermophilus and Sulfolobus tokodaii lacking SdhE homologs. Kounosu A. FEBS Lett. 588 1058-1063 (2014)
  25. On the catalytic role of the active site residue E121 of E. coli L-aspartate oxidase. Tedeschi G, Nonnis S, Strumbo B, Cruciani G, Carosati E, Negri A. Biochimie 92 1335-1342 (2010)
  26. Electron Accepting Units of the Diheme Cytochrome c TsdA, a Bifunctional Thiosulfate Dehydrogenase/Tetrathionate Reductase. Kurth JM, Brito JA, Reuter J, Flegler A, Koch T, Franke T, Klein EM, Rowe SF, Butt JN, Denkmann K, Pereira IA, Archer M, Dahl C. J. Biol. Chem. 291 24804-24818 (2016)
  27. Mutation of the heme axial ligand of Escherichia coli succinate-quinone reductase: implications for heme ligation in mitochondrial complex II from yeast. Maklashina E, Rajagukguk S, McIntire WS, Cecchini G. Biochim. Biophys. Acta 1797 747-754 (2010)
  28. Fumarate reductase: structural and mechanistic insights from the catalytic reduction of 2-methylfumarate. Wardrope C, Mowat CG, Walkinshaw MD, Reid GA, Chapman SK. FEBS Lett. 580 1677-1680 (2006)
  29. Homology modeling of T. cruzi and L. major NADH-dependent fumarate reductases: ligand docking, molecular dynamics validation, and insights on their binding modes. Merlino A, Vieites M, Gambino D, Coitiño EL. J. Mol. Graph. Model. 48 47-59 (2014)
  30. Determination of the orientation of the axial ligands and of the magnetic properties of the haems in the tetrahaem ferricytochrome from Shewanella frigidimarina. Louro RO, Pessanha M, Reid GA, Chapman SK, Turner DL, Salgueiro CA. FEBS Lett. 531 520-524 (2002)
  31. Crystal structure of an assembly intermediate of respiratory Complex II. Sharma P, Maklashina E, Cecchini G, Iverson TM. Nat Commun 9 274 (2018)
  32. Crystal structure of pyridoxine 4-oxidase from Mesorhizobium loti. Mugo AN, Kobayashi J, Yamasaki T, Mikami B, Ohnishi K, Yoshikane Y, Yagi T. Biochim. Biophys. Acta 1834 953-963 (2013)
  33. Redox behaviour of the haem domain of flavocytochrome c3 from Shewanella frigidimarina probed by NMR. Pessanha M, Rothery EL, Louro RO, Turner DL, Miles CS, Reid GA, Chapman SK, Xavier AV, Salgueiro CA. FEBS Lett. 578 185-190 (2004)
  34. Extracellular electron transfer powers flavinylated extracellular reductases in Gram-positive bacteria. Light SH, Méheust R, Ferrell JL, Cho J, Deng D, Agostoni M, Iavarone AT, Banfield JF, D'Orazio SEF, Portnoy DA. Proc Natl Acad Sci U S A (2019)
  35. Molecular interactions between multihaem cytochromes: probing the protein-protein interactions between pentahaem cytochromes of a nitrite reductase complex. Lockwood C, Butt JN, Clarke TA, Richardson DJ. Biochem. Soc. Trans. 39 263-268 (2011)
  36. Redox tuning of the catalytic activity of soluble fumarate reductases from Shewanella. Paquete CM, Saraiva IH, Louro RO. Biochim. Biophys. Acta 1837 717-725 (2014)
  37. Bridging of partially negative atoms by hydrogen bonds from main-chain NH groups in proteins: The crown motif. Leader DP, Milner-White EJ. Proteins 83 2067-2076 (2015)
  38. Expression of a metagenome-derived fumarate reductase from marine microorganisms and its characterization. Jiang C, Liu Y, Meng C, Wu L, Huang J, Deng J, Wang J, Shen P, Wu B. Folia Microbiol. (Praha) 58 663-671 (2013)
  39. Secreted Flavin Cofactors for Anaerobic Respiration of Fumarate and Urocanate by Shewanella oneidensis: Cost and Role. Kees ED, Pendleton AR, Paquete CM, Arriola MB, Kane AL, Kotloski NJ, Intile PJ, Gralnick JA. Appl Environ Microbiol 85 (2019)
  40. A Comparative Multi-Frequency EPR Study of Dipolar Interaction in Tetra-Heme Cytochromes. Hagen WR, Louro RO. Int J Mol Sci 24 12713 (2023)
  41. How an assembly factor enhances covalent FAD attachment to the flavoprotein subunit of complex II. Maklashina E, Iverson TM, Cecchini G. J Biol Chem 298 102472 (2022)
  42. Structural insight into the electron transfer pathway of a self-sufficient P450 monooxygenase. Zhang L, Xie Z, Liu Z, Zhou S, Ma L, Liu W, Huang JW, Ko TP, Li X, Hu Y, Min J, Yu X, Guo RT, Chen CC. Nat Commun 11 2676 (2020)
  43. Thermophiles; or, the Modern Prometheus: The Importance of Extreme Microorganisms for Understanding and Applying Extracellular Electron Transfer. Lusk BG. Front Microbiol 10 818 (2019)