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Metalloproteins/metalloenzymes for the synthesis of acetyl-CoA in the Wood-Ljungdahl pathway

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Abstract

This paper focuses on the group of metalloproteins/metalloenzymes in the acetyl-coenzyme A synthesis pathway of anaerobic microbes called Wood-Ljungdahl pathway, including formate dehydrogenase (FDH), corrinoid iron sulfur protein (CoFeSP), acetyl-CoA synthase (ACS) and CO dehydrogenase (CODH). FDH, a key metalloenzyme involved in the conversion of carbon dioxide to methyltetrahydrofolate, catalyzes the reversible oxidation of formate to carbon dioxide. CoFeSP, as a methyl group transformer, accepts the methyl group from CH3-H4 folate and then transfers it to ACS. CODH reversibly catalyzes the reduction of CO2 to CO and ACS functions for acetyl-coenzyme A synthesis through condensation of the methyl group, CO and coenzyme A, to finish the whole pathway. This paper introduces the structure, function and reaction mechanisms of these enzymes.

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References

  1. Berg J M, Tymoczko J L, Stryer L. Biochemistry. 5th ed. New York: W. H. Freeman and Co., 2002. 697–733

    Google Scholar 

  2. Ragsdale S W. Life with carbon monoxide. Crit Rev Biochem Mol, 2004, 39(3): 165–195

    Article  CAS  Google Scholar 

  3. Ragsdale S W. Enzymology of the Wood-Ljungdahl pathway of acetogenesis. Ann N Y Acad Sci, 2008, 1125: 129–136

    Article  CAS  Google Scholar 

  4. Muller V. Energy conservation in acetogenic bacteria. Appl Environ Microbiol, 2003, 69(11): 6345–6353

    Article  Google Scholar 

  5. Ferry J G. Formate dehydrogenase. FEMS Microbiol Rev, 1990, 7(3–4): 377–382

    CAS  Google Scholar 

  6. Popov V O, Lamzin V S. NAD(+)-dependent formate dehydrogenase. Biochem J, 1994, 301( Pt 3): 625–643

    CAS  Google Scholar 

  7. Jormakka M, Byrne B, Iwata S. Formate dehydrogenase. A versatile enzyme in changing environments. Curr Opin Struct Biol, 2003, 13(4): 418–423

    Article  CAS  Google Scholar 

  8. Ljungdahl L G. Tungsten, a biologically active metal. Trends Biochem Sci, 1976, 1: 63–65

    CAS  Google Scholar 

  9. Andreesen J R. Role of selenium, molybdenum and tungsten in anaerobes. In: Gottschalk G, Pfennig N, Werner H. eds. Anaerobiosis and Anaerobic Infection. Stuttgart: Gustav Fischer Verlag, 1979. 4–32

    Google Scholar 

  10. Ljungdahl L G. The autotrophic pathway of acetate synthesis in acetogenic bacteria. Annu Rev Microbiol, 1986, 40: 415–450

    Article  CAS  Google Scholar 

  11. Diekert G, Wohlfarth G. Metabolism of homoacetogens. Antonie van Leeuwenhoek, 1994, 66: 209–221

    Article  CAS  Google Scholar 

  12. Ljungdahl L G. Formate dehydrogenases: Role of molybdenum, tungsten and selenium. In: Coughlan M P, ed. Molybdenum and Molybdenum-Containing Enzymes. New York: Pergamon Press Oxford, 1980. 463–486

    Google Scholar 

  13. Cardin C J, Mason J. Sulphate transport by rat ileum. Effect of molybdate and other anions. Biochim Biophys Acta, 1975, 394: 46–54

    Article  CAS  Google Scholar 

  14. Tishkov V I, Popov V O. Protein engineering of formate dehydro-genase. Biomol Eng, 2006, 23: 89–110

    Article  CAS  Google Scholar 

  15. Kletzin A, Adams M W W. Tungsten in biological systems. Fems Microbiol Rev, 1996, 18: 5–63

    Article  CAS  Google Scholar 

  16. Jormakka M, Byrney B, Iwata S. Formate dehydrogenase. A versatile enzyme in changing environments. Curr Opin Struc Biol, 2003, 13: 418–423

    Article  CAS  Google Scholar 

  17. Lamzin V S, Aleshin A E, Strokopytov B V, Yukhnevich M G, Popov V O, Harutyunyan E H, Wilson K S. Crystal structure of NAD-dependent formate dehydrogenase. Eur J Biochem, 1992, 206: 441–452

    Article  CAS  Google Scholar 

  18. Romão M J, Archer M, Moura I, Moura J J G, LeGall J, Engh R, Schneider M, Hof P, Huber R. Crystal structure of the xanthine oxidase-related aldehyde oxido-reductase from D. gigas. Science, 1995, 270: 1170–1176

    Article  Google Scholar 

  19. Chan M K, Mukund S, Kletzin A, Adams M W W, Rees D C. Structure of a hyperthermophilic tungstopterin enzyme, aldehyde ferredoxin oxidoreductase. Science, 1995, 267: 1463–1469

    Article  CAS  Google Scholar 

  20. Schindelin H, Kisker C, Hilton J, Rajagopalan K V, Rees D C. The overall fold of Rhodobacter sphaeroides DMSO reductase is similar to that of FDHH. Science, 1996, 272: 1615–1622

    Article  CAS  Google Scholar 

  21. Huber R, Hof P, Duarte R O, Moura J J G, Moura I, Liu M Y, LeGall J, Hille R, Archer M, Romão M J. A structure-based catalytic mechanism for the xanthine oxidase family of molybdenum enzymes. Proc Natl Acad Sci USA, 1996, 93: 8846–8851

    Article  CAS  Google Scholar 

  22. Boyington J C, Gladyshev V N, Khangulov S V, Stadtman T C, Sun P D. Crystal structure of formate dehydrogenase H: Catalysis involving Mo, molybdopterin, selenocysteine, and an Fe4S4 cluster. Science, 1997, 275: 1305–1308

    Article  CAS  Google Scholar 

  23. Jormakka M, Tornroth S, Byrne B, Iwata S. Molecular basis of proton motive force generation: Structure of formate dehydrogenase-N. Science, 2002, 295: 1863–1868

    Article  Google Scholar 

  24. Raaijmakers H, Macieira S, Dias J M, Teixeira S, Bursakov S, Huber R, Moura J J, Moura I, Romao M J. Gene sequence and the 1.8 A crystal structure of the tungsten-containing formate dehydrogenase from desulfovibrio gigas. Structure, 2002, 10: 1261–1272

    Article  CAS  Google Scholar 

  25. Filippova E V, Polyakov K M, Tikhonova T V, Stekhanova T N, Boiko K M, Popov V O. Structure of a new crystal modification of the bacterial NAD-dependent formate dehydrogenase with a resolution of 2.1A. Crystallogr Rep, 2005, 50(5): 796–800

    Article  CAS  Google Scholar 

  26. Filippova E V, Polyakov K M, Tikhonova T V, Stekhanova T N, Boiko K M, Sadykhov I G, Tishkov V I, Popov V O, Labru N. Crystal structures of complexes of NAD+-dependent formate dehydrogenase from methylotrophic bacterium Pseudomonas sp. 101 with formate. Crystallogr Rep, 2006, 51(4): 627–631

    Article  CAS  Google Scholar 

  27. Böck A, Stadtman T C. Selenocysteine, a highly specific component of certain enzymes, is incorporated by a UGA-directed co-translational mechanism. Biofactors, 1988, 1(3): 245–250

    Google Scholar 

  28. Humphrey W, Dalke A, Schulten K. VMD-visual molecular dynamics. J Molec Graphics, 1996, 14: 33–38

    Article  CAS  Google Scholar 

  29. Khangulov S V, Gladyshev V N, Dismukes G C, Stadtman T C. Selenium-containing formate dehydrogenase H from Escherichia coli: A molybdopterin enzyme that catalyzes formate oxidation without oxygen transfer. Biochemistry, 1998, 37: 3518–3528

    Article  CAS  Google Scholar 

  30. Yamamoto I, Saiki T, Liu S M, Ljungdahl L G. Purification and properties of NADP-dependent formate dehydrogenase from Clostridium thermoaceticum, a tungsten-selenium-iron protein. J Biol Chem, 1983, 258(3): 1826–1832

    CAS  Google Scholar 

  31. Hu S I, Pezacka E, Wood H G. Acetate synthesis from carbon monoxide by Clostridium thermoaceticum. Purification of the corrinoid protein. J Biol Chem, 1984, 259: 8892–8897

    CAS  Google Scholar 

  32. Maupin F J, Ferry J G. Analysis of the CO dehydrogenase/acetylcoenzyme A synthase operon of Methanosarcina thermophila. J Bacteriol, 1996, 178: 340–346

    Google Scholar 

  33. Svetlitchnyi V, Dobbek H, Meyer-Klaucke W, Meins T, Thiele B, Romer P, Huber R, Meyer O. A functional Ni-Ni-[4Fe-4S] cluster in the monomeric acetyl-CoA synthase from Carboxydothermus hydrogenoformans. Proc Natl Acad Sci USA, 2004, 101: 446–451

    Article  CAS  Google Scholar 

  34. Svetlitchnaia T, Svetlitchnyi V, Meyer O, Dobbek H. Structural insights into methyltransfer reactions of a corrinoid iron-sulfur protein involved in acetyl-CoA synthesis. Proc Natl Acad Sci USA, 2006, 103 (39): 14331–14336

    Article  CAS  Google Scholar 

  35. Funk T, Gu W W, Friedrich S, Wang H X, Gencic S, Grahame D A, Cramer S P. Chemically distinct Ni sites in the A-cluster in subunit β of the acetyl-CoA decarbonylase/synthase complex from Methanosarcina thermophila: Ni L-edge absorption and X-ray magnetic circular dichroism analyses. J Am Chem Soc, 2004, 126 (1): 88–95

    Article  CAS  Google Scholar 

  36. Dobbek H, Svetlitchnyi V, Gremer L, Huber R, Meyer O. Crystal structure of a carbon monoxide dehydrogenase reveals a [Ni-4Fe-5S] cluster. Science, 2001, 293: 1281–1285

    Article  CAS  Google Scholar 

  37. Drennan C L, Heo J, Sintchak M D, Schreiter E, Ludden P W. Redox-dependent activation of CO dehydrogenase from Rhodospirillum rubrum. Proc Natl Acad Sci USA, 2001, 98: 11973–11978

    Article  CAS  Google Scholar 

  38. Doukov T I, Iverson T M, Seravalli J, Ragsdale S W, Drennan C L. A Ni-Fe-Cu center in a bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase. Science, 2002, 298: 567–572

    Article  CAS  Google Scholar 

  39. Darnault C, Volbeda A, Kim E J, Legrand P, Vernede X, Lindahl P A, Fontecilla-Camps J C. Ni-Zn-[Fe-4-S-4] and Ni-Ni-[Fe-4.S-4] clusters in closed and open subunits of acetyl-CoA synthase/carbon monoxide dehydrogenase. Nat Struct Mol Biol, 2003, 10(4): 271–279

    Article  CAS  Google Scholar 

  40. Svetlitchnyi V, Dobbek H, Meyer-Klaucke W, Meins T, Thiele B, Romer P, Huber R, Meyer O. Life on carbon monoxide: X-ray structure of Rhodospirillum rubrum Ni-Fe-S carbon monoxide dehydrogenase. Proc Natl Acad Sci USA, 2004, 101: 446–451

    Article  CAS  Google Scholar 

  41. Jeoung J H, Dobbek H. Carbon dioxide activation at the Ni, Fe-cluster of anaerobic carbon monoxide dehydrogenase. Science, 2007, 318: 1461–1464

    Article  CAS  Google Scholar 

  42. Lindahl P A. The Ni-containing carbon monoxide dehydrogenase family: Light at the end of the tunnel. Biochemistry, 2002, 41: 2097–2105

    Article  CAS  Google Scholar 

  43. Kim E J, Feng J, Bramlett M R, Lindahl P A. Carbon monoxide dehydrogenase from Rhodospirillum rubrum: Effect of redox potential on catalysis. Biochemistry, 2004, 43: 5728–5734

    Article  CAS  Google Scholar 

  44. Hu Z, Spangler N J, Anderson M E, Xia J, Ludden P W, Lindahl P A, Munck E. Nature of the C-cluster in Ni-containing carbon monoxide dehydrogenases. J Am Chem Soc, 1996, 118: 830–845

    Article  CAS  Google Scholar 

  45. DeRose V J, Telser J, Anderson M E, Lindahl P A, Hoffman B M. A multinuclear ENDOR study of the C-cluster in CO dehydrogenase from Clostridium thermoaceticum: Evidence for HxO and histidine coordination to the [Fe4S4] center. J Am Chem Soc, 1998, 120: 8767–8776

    Article  CAS  Google Scholar 

  46. Fraser D M, Lindahl P A. Evidence for a proposed intermediate redox state in the CO/CO2 active site of acetyl-CoA synthase (carbon monoxide dehydrogenase) from Clostridium thermoaceticum. Biochemistry, 1999, 38: 15706–15711

    Article  CAS  Google Scholar 

  47. Loke H K, Tan X S, Lindahl P A. Genetic construction of truncated and chimeric metalloproteins derived from the alpha subunit of acetyl-CoA synthase from Clostridium thermoaceticum. J Am Chem Soc, 2002, 124(29): 8667–8672

    Article  CAS  Google Scholar 

  48. Tan X S, Bramlett M R, Lindahl P A. Effect of Zn on acetyl coenzyme a synthase: Evidence for a conformational change in the a subunit during catalysis. J Am Chem Soc, 2004, 126(19): 5954–5955

    Article  CAS  Google Scholar 

  49. Bramlett M R, Tan X S, Lindahl P A. Inactivation of acetyl-CoA synthase/carbon monoxide dehydrogenase by copper. J Am Chem Soc, 2003, 125(31): 9316–9317

    Article  CAS  Google Scholar 

  50. Tan X S, Loke H K, Fitch S, Lindahl P A. The tunnel of the acetyl-CoA synthase/carbon monoxide dehydrogenase regulates delivery of CO to the active site. J Am Chem Soc, 2005, 127(16): 5833–5839

    Article  CAS  Google Scholar 

  51. Tan X S, Volbeda A, Fontecilla-Camps J C, Lindahl P A. Function of the tunnel in acetyl-coenzyme A synthase/carbon monoxide dehydrogenase. J Biol Inorg Chem, 2006, 11(3): 371–378

    Article  CAS  Google Scholar 

  52. Tan X S, Kagiampakis I, Surovtsev I V, Demeler B, Lindahl P A. Nickel-dependent oligomerization of the alpha subunit of acetyl-coenzyme a synthase/carbon monoxide dehydrogenase. Biochemistry, 2007, 46: 11606–11613

    Article  CAS  Google Scholar 

  53. Tan X S, Surovtsev I V, Lindahl P A. Kinetics of CO insertion and acetyl-group transfer steps, and a model of the acetyl-coenzyme A synthase catalytic mechanism. J Am Chem Soc, 2006, 128(37): 12331–12338

    Article  CAS  Google Scholar 

  54. Tan X S, Christopher S, Lindahl P A. Stopped-flow kinetic of methyl group transfer between corrinoid-iron-sulfur protein and acetyl-coenzyme A synthase from Clostridium thermoaceticum. J Am Chem Soc, 2002, 124(22): 6277–6284

    Article  CAS  Google Scholar 

  55. Tan X S, Sewell C, Yang Q W, Lindahl P A. Reduction and methyl transfer kinetics of alpha subunit from acetyl-coenzyme A synthase. J Am Chem Soc, 2003, 125(2): 318–319

    Article  CAS  Google Scholar 

  56. Seravalli J, Ragsdale S W. Pulse-chase studies of the synthesis of acetyl-CoA by carbon monoxide dehydrogenase/acetyl-CoA synthase. Evidence for a random mechanism of methyl and carbonyl addition. J Biol Chem, 2008, 283(13): 8384–8394

    CAS  Google Scholar 

  57. Grahame D A. Acetate C-C bond formation and decomposition n the anaerobic world: The structure of a central enzyme and its key active-site metal cluster. Trends Biochem Sci, 2003, 28(5): 221–224

    Article  CAS  Google Scholar 

  58. Grahame D A. Catalysis of acetyl-CoA cleavage and tetrahydrosarcinapterin methylation by a cabon-monoxide dehydrogenase-corrinoid enzyme complex. J Biol Chem, 1991, 266: 22227–22233

    CAS  Google Scholar 

  59. Grahame D A, DeMoll E. Partial reactions catalyzed by protein components of the acetyl-CoA decarbonylase synthase enzyme complex from Methanosarcina barkeri. J Biol Chem, 1996, 271(14): 8352–8358

    Article  CAS  Google Scholar 

  60. Bhaskar B, DeMoll E, Grahame D A. Redox-dependent acetyl transfer partial reaction of the acetyl-CoA decarbonylase/synthase complex: Kinetics and mechanism. Biochemistry, 1998, 37: 14491–14499

    Article  CAS  Google Scholar 

  61. Kocsis E, Kessel M, DeMoll E, Grahame D A. Structure of the Ni/Fe-S protein subcomponent of the acetyl-CoA decarbonylase/synthase complex from Methanosarcina thermophila at 26-angstrom resolution. J Struct Biol, 1999, 128: 165–174

    Article  CAS  Google Scholar 

  62. Balbo P, Oliveira M. Crystallization and preliminary X-ray data of the α2ε2 subcomponent of the acetyl-CoA decarbonylase/synthase multienzyme complex from Methanosarcina thermophila. Acta Crystallogr D Biol Crystallogr, 2003, 59: 721–723

    Article  Google Scholar 

  63. Sebaihia M, Wren B W, Mullany P, Fairweather N F, Minton N, Stabler R, Thomson N R, Roberts A P, Cerdeno-Tarraga A M, Wang H, Holden M T, Wright A, Churcher C, Quail M A, Baker S, Bason N, Brooks K, Chillingworth T, Cronin A, Davis P, Dowd L, Fraser A, Feltwell T, Hance Z, Holroyd S, Jagels K, Moule S, Mungall K, Price C, Rabbinowitsch E, Sharp S, Simmonds M, Stevens K, Unwin L, Whithead S, Dupuy B, Dougan G, Barrell B, Parkhill J. The multidrug-resistant human pathogen Clostridium difficile has a highly mobile mosaic genome. Nat Genet, 2006, 38 (7): 779–786

    Article  Google Scholar 

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Correspondence to XiangShi Tan.

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Supported by the National Natural Science Foundation of China (Grant No. 20771029), Shanghai Pujiang Talent Project (Grant No. 08PJ14017) and Shanghai Leading Academic Discipline Project (Grant No. B108)

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Zhu, X., Tan, X. Metalloproteins/metalloenzymes for the synthesis of acetyl-CoA in the Wood-Ljungdahl pathway. Sci. China Ser. B-Chem. 52, 2071–2082 (2009). https://doi.org/10.1007/s11426-009-0082-3

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