Publikationsserver der Universitätsbibliothek Marburg
Titel:Charakterisierung der an der Biosynthese des Cofaktors der [Fe]-Hydrogenase Hmd beteiligten Hcg-Proteine
Autor:Bai, Liping
Weitere Beteiligte: Shima, Seigo (Dr.)
Veröffentlicht:2017
URI:https://archiv.ub.uni-marburg.de/diss/z2017/0665
URN: urn:nbn:de:hebis:04-z2017-06654
DOI: https://doi.org/10.17192/z2017.0665
DDC: Biowissenschaften, Biologie
Titel (trans.):Characterization of the Hcg proteins involved in [Fe]-hydropgenase cofactor biosynthesis
Publikationsdatum:2017-10-04
Lizenz:https://rightsstatements.org/vocab/InC-NC/1.0/

Dokument

Schlagwörter:
Biosynthese, Hydrogenase, Cofacor

Summary:
[Fe]-hydrogenase (Hmd) catalyzes the reduction of methenyl-H4MPT+ to methylene-H4MPT using H2 as electron donor in the hydrogenotrophic methanogenic pathway. The production of Hmd was upregulated when the cell was grown under Ni-limiting environment. Hmd is composed of homodimer; the active sites are located at the cleft formed by the N-terminal domain and central domain. The N-terminal domain binds an iron-guanylylpyridinol (FeGP) cofactor, which is prosthetic group of this enzyme. The FeGP cofactor is composed of a low spin FeII ligated with two CO, an acyl-C and pyridinol-N; in addition, Cys-S and a solvent are bound to the iron site in the enzyme. The pyridinol ring is substituted with GMP moiety and two methyl groups. Genome analysis indicated that there are seven conserved genes which is named hcg gene cluster containing hcgAG and hmd genes. Therefore, it was predicted that the hcg cluster is responsible for biosynthesis of the FeGP cofactor. From the hcg genes sequences, we could not deduce the function of the proteins. However, using the “structure to function” strategy and biochemical assays, we could identify the function of some Hcg proteins. In this thesis, I describe the function of HcgC based on crystal structure and biochemical analyses. The isotope-labeling experiment indicated that the C3 methyl group comes from methionine, probably via S-adenosylmethionine (SAM). Structure comparisons of HcgC with other proteins suggested similarity of HcgC to SAM-dependent methyltransferases. Co-crystallization of HcgC and SAM revealed that SAM binds to the active site of HcgC. Docking simulation with a possible methyl-acceptor pyridinol suggested that the binding site of the pyridinol. The predicted substrate pyridinol was chemically synthesized and the enzyme activity was determined. The structure of the HcgC-reaction product was determined by NMR, which confirmed that HcgC transfer the methyl group from SAM to C3 of pyridinol. In order to analyze the catalytic mechanism of HcgC, co-crystallizaiton of HcgC, pyridinol, SAM or SAH was performed. The substrate binding site structure showed that seven water molecules connected pyridinol to protein. The only interaction of pyridinol with amino acid side chain was Thr179-OH. The C3 of pyridinol was close to the sulfur of SAH. In the crystal structure, there was no amino acid, which functions as general base of the typical methyl-transfer reaction. We proposed that the water molecules stabilize the deprotonated form of pyridinol by resonance effect, which increases the nucleophilicity of C3. Mutation analysis supported the essential contribution of the water molecules.

Bibliographie / References

  1. [145] Bai, L., Fujishiro, T., Huang, G., Koch, J., Takabayashi, A., Yokono, M., Tanaka, A., Xu, T., Hu, X., Ermler, U., Shima, S. (2017) Towards artificial methanogenesis: biosynthesis of the [Fe]-hydrogenase cofactor and characterization of the semi-synthetic hydrogenase. Faraday Discuss., doi: 10.1039/c6fd00209a. [Epub ahead of print]
  2. [42] Berger, S., Welte, C., Deppenmeier, U. (2012) Acetate activation in Methanosaeta thermophila: characterization of the key enzymes pyrophosphatase and acetyl-CoA synthetase. Archaea, 2012: 315-153.
  3. [58] Dai, Y. R., Reed, D. W., Millstein, J. H., Hartzall, P. L., Grahame, D. A., deMoll, E. (1998) Acetyl-CoA decarbonylase/synthase complex from Archaeoglobus fulgidus. Arch Microbiol., 169: 525-529.
  4. [147] Reyda, M. R., Fugate, C. J., Jarrett, J. T. (2009) A complex between biotin synthase and the iron-sulfur cluster assembly chaperone HscA that enhances in vivo cluster assembly. Biochemistry, 48: 10782-10792.
  5. [131] Schwörer. B, Thauer, R. K. (1991) Activities of formylmethanofuran dehydrogenase, methylenetetrahydromethanopterin dehydrogenase, methylenetetrahydro-methanopterin reductase, and heterodisulfide reductase in methanogenic bacteria. Arch. Microbiol., 155: 459-465.
  6. [44] Jetten, M. S., Fluit, T. J., Stams, A. J. M., Zehnder, A. J. B. (1992) A fluorideinsensitive inorganic pyrophosphatase isolated from Methanothrix soehngenii. Arch. Microbiol., 157: 284-289.
  7. [136] Xu, T., Yin, C. J., Wodrich, M. D., Mazza, S., Schultz, K. M., Scopelliti, R., Hu, X. (2016) A functional model of [Fe]-hydrogenase. J. Am. Chem. Soc., 138: 3270-3273.
  8. [81] Nicolet, Y., Martin, L., Tron, C., Fontecilla-Camps, J. C. (2010) A glycyl free radical as the precursor in the synthesis of carbon monoxide and cyanide by the [FeFe]-hydrogenase maturase HydG. FEBS Lett., 584: 4197-202.
  9. [8] Boetius, A., Ravenschlag, K., Schubert, C. J., Rickert, D., Widdel, F., Gieseke, A., Amann, R., Jorgensen, B. B., Witte, U., Pfannkuche, O. (2000) A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature, 407: 623-626.
  10. [9] Haroon, M. F., Hu, S., Shi, Y., Imelfort, M., Keller, J., Hugenholtz, P., Yuan, Z., Tyson, G. W. (2013) Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature, 500: 567-570.
  11. [141] Magalon, A., Böck, A. (2000) Analysis of the HypC-HycE complex, a key intermediate in the assembly of the metal center of the Escherichia coli hydrogenase 3. J. Biol. Chem., 275: 21114-21120.
  12. [98] Fujishiro, T., Ermler, U., Shima, S. (2014) A possible iron delivery function of the dinuclear iron center of HcgD in [Fe]-hydrogenase cofactor biosynthesis. FEBS Lett., 588: 2789-2793.
  13. [125] Grove, T. L. Benner, J. S., Radle, M. I., Ahlum, J. H., Landgraf, B. J., Kerbs, C., Booker, S. J. (2011) A radically different mechanism for S-adenosylmethioninedependent methyltransferase. Science, 332: 604-607.
  14. [110] Brandford, M. M. (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein ultilizing the principle of protein-dye binding. Anal. Biochem., 72: 248-254.
  15. [118] Liscombe, D. K., Louie, G. V., Noel, J. P. (2012) Architectures, mechanisms and molecular evolution of natural product methyltransferases. Nat. Prod. Rep., 29: 1238-1250.
  16. [133] Shima, S., Thauer, R. K. (2007) A third type of hydrogenase catalyzing H2 activation. Chem. Rec., 7: 37-46.
  17. [82] Driesener, R. C., Duffus, B. R., Shepard, E. M., Bruzas, I. R., Duschene, K. S., Coleman, N. J., Marrison, A. P., Salvadori, E., Kay, C. W., Peters, J. W., Broderick, J. B., Roach, P. L. (2013) Biochemical and kinetic characterization of radical S-adenosyl-L-methionine enzyme HydG. Biochemistry, 52: 8696-8707.
  18. [7] Thauer, R. K. (1998) Biochemistry of methanogenesis: a tribute to marjory stephenson. Microbiology, 144: 2377-2406.
  19. [17] Welte, C., Deppenmeier, U. (2014) Bioenergetics and anaerobic respiratory chains of aceticlastic methanogens. Biochim. Biophys. Acta, 1837: 1130-1147.
  20. [72] Berggren, G., Adamska, A., Lambertz, C., Simmons, T. R., Esselborn, J., Atta, M., Gambarelli, S., Mouesca, J. M., Reijerse, E., Lubitz, W., Happe, T., Artero, V., Fontecave, M. (2013) Biomimetic assembly and activation of [FeFe]- hydrogenases. Nature, 499: 66-70.
  21. [102] Suess, D. L., Kuchenreuther, J. M., De La Paz, L., Swartz, J. R., Britt, R. D. (2016) Biosynthesis of the [FeFe] Hydrogenase H Cluster: a central role for the radical SAM enzyme HydG. Inorg. Chem., 55: 478-487.
  22. [93] Schick, M., Xie, X., Ataka, K., Kahnt, J., Linne, U., Shima, S. (2012) Biosynthesis of the iron-guanylylpyridinol cofactor of [Fe]-hydrogenase in methanogenic archaea as elucidated by stable-isotope labeling. J. Am. Chem. Soc., 134: 3271-3280.
  23. [148] Fugate, C. J., Jarrett, J. T. (2012) Biotin synthase: insights into radical-mediated carbon-sulfur bond formation. Biochim. Biophys. Acta, 1824: 1213-1222.
  24. [62] Paschos, A., Glass, R. S., Böck, A. (2001) Carbamoylphosphate requirement for synthesis of the active center of [NiFe]-hydrogenase. FEBS Lett., 488: 9-12.
  25. [16] Kühn, W., Gottschalk, G. (1983) Characterization of the cytochromes occurring in Methanosarcina species. Eur. J. Biochem., 135: 89-94.
  26. [50] Murakami, E., Deppenmeier, U., Ragsdale, S. W. (2001) Characterization of the intramolecular electron transfer pathway from 2-hydroxyphenazine to the heterodisulfide reductase from Methanosarcina thermophila. J. Biol. Chem., 276: 2432-2439.
  27. [67] Leipe, D. D., Wolf, Y. I., Koonin, E. V., Aravind, L. (2002) Classification and evolution of P-loop GTPases and related ATPase. J. Mol. Biol., 317: 41-72.
  28. [79] Pagnier, A., Martin, L., Zeppieri, L., Nicolet, Y., Fontecilla-Camps, J. C. (2016) CO and CN− syntheses by [FeFe]-hydrogenase maturase HydG are catalytically differentiated events. Proc. Natl. Acad. Sci. USA, 113: 104-109.
  29. [31] Vaupel, M., Thauer, R. K. (1995) Coenzyme F420-dependent N5,N10- methylenetetrahydromethanopterin reductase (Mer) from Methanobacterium thermoautotrophicum strain Marburg. Cloning, sequencing, transcriptional analysis, and functional expression in Escherichia coli of the mer gene. Eur. J. Biochem., 231: 773-778.
  30. [86] Zhang, Y., Rodionov, D. A., Gelfand, M. S., Gladyshev, V. N. (2009) Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization. BMC Genomics, 10: 78.
  31. [97] Galperin, M. Y., Koonin, E. V. (2004) 'Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucleic Acids Res., 32: 5452- 5463.
  32. [115] Emsley, P., Cowtan, K. (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr. D, 60: 2126-2132.
  33. [64] Bürstel, I., Siebert, E., Frielingsdorf, S., Zebger, I., Friedrich, B., Lenz, O. (2017) CO synthesized from the central one-carbon pool as sorce for the iron carbonyl in O2-tolerant [NiFe]-hydrogenase. Proc. Natl. Acad. Sci. USA, 113.
  34. [39] Kaster, A. K., Moll, J., Parey, K., Thauer, R. K. (2011) Coupling of ferredoxin and heterodisulfide reduction via electron bifurcation in hydrogenotrophic methanogenic archaea. Proc. Natl. Acad. Sci. USA, 108: 2981-2986.
  35. [23] Shima, S., Thauer, R. K., Michel, H., Ermler, U. (1996) Crystallization and preliminary X-ray diffraction studies of formylmethanofuran: tetrahydromethanopterin formyltransferase from Methanopyrus kandleri. Proteins, 26: 118-120.
  36. [32] Shima, S., Goubeaud, M., Vinzenz, D., Thauer, R. K., Ermler, U. (1997) Crystallization and preliminary X-ray diffraction studies of methyl-coenzyme M reductase from Methanobacterium thermoautotrophicum. J. Biochem., 121: 829-830.
  37. [36] Ermler, U., Grabarse, W., Shima, S., Goubeaud, M., Thauer, R. K. (1997) Crystal structure of methyl-coenzyme M reductase: the key enzyme of biological methane formation. Science, 278: 1457-1462.
  38. [121] Dai, Y. N., Zhou, K., Cao, D. D., Jiang, Y. L., Meng, F., Chi, C. B., Ren, Y. M., Chen, Y., Zhou, C. Z. (2014) Crystal structures and catalytic mechanism of the C-methyltransferase Coq5 provide insights into a key step of the yeast coenzyme Q synthesis pathway. Acta Crystallogr D, 70: 2085-2092.
  39. [83] Suess, D. L., Burstel, I., De La Paz, L., Kuchenreuther, J. M., Pham, C. C., Cramer, S. P., Swartz, J. R., Britt, R. D. (2015) Cysteine as a ligand platform in the biosynthesis of the FeFe hydrogenase H cluster. Proc. Natl. Acad. Sci. USA, 112: 11455-11460.
  40. [47] Oremland, R. S., Kiene, R. P., Mathrani, I., Whiticar, M. J., Bonne, D. (1989) Description of an estuarine methylotrophic Methanogen which grow on dimethyl sulfide. Appl. Environ. Microbiol., 55: 994-1002.
  41. [19] Boone, D. R., Johnson, R. L., Liu, Y. (1989) Diffusion of the interspecies electron carriers H2 and formate in methanogenic ecosystems and its implications in the measurement of Km for H2 or formate uptake. Appl. Environ. Microbiol., 55: 1735-1741.
  42. [70] Posewitz, M. C., King, P. W., Smolinski, S. L., Zhang, L., Seibert, M., Ghirardi, M. L. (2004) Discovery of two novel radical S-adenosylmethionine proteins required for the assembly of an active [Fe] hydrogenase. J. Biol. Chem., 279: 25711-25720.
  43. [15] Kühn, W., Fiebig, K., Hippe, H., Mah, R. A., Huster, B. A., Gottschalk, G. (1983) Distribution of cytochromes in methanogenic bacteria. FEMS Microbiol. Lett., 20: 407-410.
  44. [124] Buckel, W., Thauer, R. K. (2011) Dual role of S-adenosylmethionine (SAM+) in the methylation of sp2-hybridized electrophilic carbons. Angew. Chem., Int. Ed., 50: 10492-10494.
  45. [51] Ide, T., Baümer, S., Deppenmeier, U. (1999) Energy conservation by the H2:Heterodisulfide oxidoreductase from Methanosarcina mazei Gö1: identification of two Proton-translocating segments. J. Bacteriol., 181: 4076- 4080.
  46. [55] Buckel, W., Thauer, R. K. (2013) Energy conservation via electron bifurcating ferredoxin reduction and proton/Na+ translocating ferredoxin oxidation. Biochim. Biophys. Acta, 1827: 94-113.
  47. [56] Shima, S. (2014) Enzyme chemistry of methanogenesis and anaerobic oxidation of methane. Kagakutoseibutsu, 52: 307-312.
  48. [41] Ferry, J. G. (1997) Enzymology of the fermentation of acetate to methane by Methanosarcina thermophila. BioFactors, 6: 25-35.
  49. [91] Shima, S., Schick, M., Kahnt, J., Ataka, K., Steinbach, K., Linne, U. (2012) Evidence for acyl-iron ligation in the active site of [Fe]-hydrogenase provided by mass spectrometry and infrared spectroscopy. Dalton Trans., 41: 767-771.
  50. [69] Peters, J. W., Schut, G. J., Boyd, E. S., Mulder, D. W., Shepard, E. M., Broderick, J. B., King, P. W., Adams, M. W. (2015) [FeFe]- and [NiFe]-hydrogenase diversity, mechanism, and maturation. Biochim. Biophys. Acta, 1853: 1350- 1369.
  51. [74] Betz, J. N., Boswell, N. W., Fugate, C. J., Holliday, G. L., Akiva, E., Scott, A. G., Babbitt, P. C., Peters, J. W., Shepard, E. M., Broderick, J. B. (2015) [FeFe]- hydrogenase maturation: insights into the role HydE plays in dithiomethylamine biosynthesis. Biochemistry, 54: 1807-1818.
  52. [111] Hennessy, D. J., Reid, G.R., Smith, F.E., Thompson, S.L. (1984) Ferene-a new spectrophotometric reagent for iron. Can. J. Chem., 62: 721-724.
  53. [54] Osyczka, A., Moser, C. C., Dutton, P. L. (2005) Fixing the Q cycle. Trends Biochem. Sci., 30: 176-182.
  54. [22] Shima, S., Weiss, D. S., Thauer, R. K. (1995) Formylmethanofuran:tetrahydromethanopterin formyltransferase (Ftr) from the hyperthermophilic Methanopyrus kandleri Cloning, sequencing and functional expression of the ftr gene and one-step purification of the enzyme overproduced in Escherichia coli. Eur. J. Biochem., 230: 906-913.
  55. [105] Takahashi, Y., Nakamura, M. (1999) Functional assignment of the ORF2-iseSiscU-iscA-hscB-hscA-fdx-ORF3 gene cluster involved in the assembly of Fe-S clusters in Escherichia coli. J. Bacteriol., 126: 917-926.
  56. [143] King, P. W., Posewitz, M. C., Ghirardi, M. L., Seibert, M. (2006) Functional Studies of [FeFe] Hydrogenase Maturation in an Escherichia coli Biosynthetic System. J. Bacteriol., 188: 2163-2172.
  57. [30] Afting, C., Hohheimer, A., Thauer, R. K. (1998) Function of H2-forming methylenetetrahydromethanopterin dehydrogenase from Methanobacterium thermoautotrophicum in coenzyme F420 reduction with H2. Arch. Microbiol., 169: 206-210.
  58. [40] Ferry, J. G. (2011) Fundamentals of methanogenic pathways that are key to the biomethanation of complex biomass. Curr. Opin. Biotechnol., 22: 351-357.
  59. [14] Jussofie, A., Gottschalk, G. (1986) Further studies on the distribution of cytochromes in methanogens. FEMS Microbiol. Lett., 37: 15-18.
  60. [3] Hasen, J., Fung, I., Lacis A., Rind, D., Lebedeff, S., Ruedy, R., Russell, G. (1988) Global climate changes as forest by goddard institute for space studies three-dimensional model. J. Geoohys. Res, 93: 9431-9464.
  61. [20] Widdel, F. (1986) Growth of methanogenic bacteria in pure culture with 2- propanol and other alcohols as hydrogen donors. Appl. Environ. Microbiol., 51: 1056-1062.
  62. [48] Schönheit, P., Moll, J., Thauer, R. K. (1980) Growth parameters (Ks, µmax, Ys) of Methanobacterium thermoautotrophium. Arch. Microbiol., 127: 59-65.
  63. [27] Zirngibl, C., Van Dongen, W., Schworer, B., Von Bunau, R., Richter, M., Klein, A., Thauer, R. K. (1992) H2-forming methylenetetrahydromethanopterin dehydrogenase, a novel type of hydrogenase without iron-sulfur clusters in methanogenic archaea. Eur J Biochem, 208: 511-520.
  64. [106] Huang, H., Hu, L., Yu, W., Li, H., Tao, F.,Xie, H.,Wang, S. (2016) Heterologous overproduction of 2[4Fe4S]- and [2Fe2S]-type clostridial ferredoxins and [2Fe2S]-type agrobacterial ferredoxin. Protein Expr. Purif., 121: 1-8.
  65. [38] Thauer, R. K., Kaster, A. K., Goenrich, M., Schick, M., Hiromoto, T., Shima, S. (2010) Hydrogenases from methanogenic archaea, nickel, a novel cofactor, and H2 storage. Annu. Rev. Biochem., 79: 507-536.
  66. [103] McGlynn, S. E., Boyd, E. S., Shepard, E. M., Lange, R. K., Gerlach, R., Broderick, J. B., Peters, J. W. (2010) Identification and characterization of a novel member of the radical AdoMet enzyme superfamily and implications for the biosynthesis of the Hmd hydrogenase active site cofactor. J. Bacteriol., 192: 595-598.
  67. [129] Fujishiro, T., Bai, L., Xu, T., Xie, X., Schick, M., Kahnt, J., Rother, M., Hu, X., Ermler, U., Shima, S. (2016) Identification of HcgC as a SAM-dependent pyridinol methyltransferase in [Fe]-hydrogenase cofactor biosynthesis. Angew. Chem., Int. Ed., 55: 9648-9651.
  68. [33] Harms, U., Thauer, R. K. (1997) Identification of the active site histidine in the corrinoid protein MtrA of the energy-conserving methyltransferase complex from Methanobacterium thermoautotrophicum. Eur. J. Biochem., 250: 783-788.
  69. [94] Fujishiro, T., Tamura, H., Schick, M., Kahnt, J., Xie, X., Ermler, U., Shima, S. (2013) Identification of the HcgB enzyme in [Fe]-hydrogenase-cofactor biosynthesis. Angew. Chem. Int. Ed., 52: 12555-12558.
  70. [107] Tartof, K. D., Hobbs, C. A. (1987) Improved media for growing plasmid and cosmid clones. Bethesda Res. Lab. Focus: 9-12.
  71. [108] Bowen, T. L., Whitman, W. B. (1987) Incorporation of exogenous purines and pyrimidines by Methanococcus voltae and isolation of analog-resistant mutants. Appl. Environ. Microbiol., 53: 1822-1826.
  72. [45] Hagemeier, C. H., Krer, M., Thauer, R. K., Warkentin, E., Ermler, U. (2006) Insight into the mechanism of biological methanol activation based on the crystal structure of the methanol-cobalamin methyltransferase complex. Proc. Natl. Acad. Sci. USA, 103: 18917-18922.
  73. [63] Drapal, N., Böck, A. (1998) Interaction of the hydrogenase accessory protein HypC with HycE, the large subunit of Escherichia coli hydrogenase 3 during enzyme maturation. Biochemistry, 37: 2941-2948.
  74. [137] Schwartz, L., Eilers, G., Eriksson, L., Gogoll, A., Lomoth, R., Ott, S. (2006) Iron hydrogenase active site mimic holding a proton and a hydride. Chem. Commun.: 520-522.
  75. [109] Moore, B. C., Leigh, J. A., (2005) Markerless mutagenesis in Methanococcus maripaludis demonstrates roles for alanine dehydrogenase, alanine racemase, and alanine permease. J. Bacteriol. 187: 972-979.
  76. [59] Böck, A., King, P. W., Blokesch, M., Posewitz, M. C. (2006) Maturation of hydrogenases. Advan. Microb. Physiol., 51: 1-71.
  77. [6] Thauer, R. K., Shima, S. (2008) Methane as fuel for anaerobic microorganisms. Ann. N. Y. Acad. Sci., 1125: 158-170.
  78. [11] Evans, P. N., Parks, D. H., Chadwick, G. L., Robbins, S. J., Orphan, V. J., Golding S. D., Tyson, G. W. (2015) Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics. Science, 1: 1-9.
  79. [5] Thauer, R. K., Kaster, A. K., Seedorf, H., Buckel, W., Hedderich, R. (2008) Methanogenic archaea: ecologically relevant differences in energy conservation. Nat. Rev. Microbiol., 6: 579-591.
  80. [18] Johnes, W. J., Nagle, D. P., Whitman, W. B. (1987) Methanogens and the diversity of archaebacteria. Microbiol. Rev., 51: 135-177.
  81. [43] Smith, K. S., Ingram-Smith, C. (2007) Methanosaeta, the forgotten methanogen? Trends Microbiol., 15: 150-155.
  82. [104] Shima, S., Schick, M., Tamura, H. (2011) Methods in Enzymology. Methods Enzymol, 494: 119-137.
  83. [12] Vanwonterghem, I., Evans, P. N., Parks, D. H., Jensen, P. D., Woodcroft, B. J., Hugenholtz, P., Tyson, G. W. (2016) Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota. Nat. Microbiol., 1: 16170.
  84. [116] Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S., Richardson, D. C. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D, 66: 12-21.
  85. [128] Shima, S., Lyon, E. J., Thauer, R. K., Mienert, B., Bill, E. (2005) Mössbauer studies of the iron-sulfur cluster-free hydrogenase: the electronic state of the mononuclear Fe active site. J. Am. Chem. Soc., 127: 10430-10435.
  86. [138] Sauer, M., Böhm, R., Böck, A. (1992) Mutational analysis of the operon (hyc) determining hydrogenase 3 formation in Escherichia coli. Mol. Microbiol., 6: 1523-1532.
  87. [35] Becher, B., Müller, V., Gottschalk, G. (1992) N5-methyltetrahydromethanopterin: coenzyme M methyltransferase of Methanosarcina strain Gol is an Na+-translocating membrane protein. J. Bacteriol., 174: 7656- 7660.
  88. [24] Klein, A. R., Breitung, J., Linder, D., Stetter, K. O., Thauer, R. K. (1993) N5,N10- methenyltetrahydromethanopterin cyclohydrolase from the extremely thermophilic sulfate reducing Archaeoglobus fulgidus: comparison of its properties with those of the cyclohydrolase from the extremely thermophilic Methanopyrus kandleri. Arch. Microbiol., 159: 213-219.
  89. [99] Burroughs, A. M., Iyer, L. M., Aravind, L. (2009) Natural history of the E1-like superfamily: implication for adenylation, sulfur transfer, and ubiquitin conjugation. Proteins, 75: 895-910.
  90. [140] Hube, M., Blokesch, M., Böck, A. (2002) Network of hydrogenase maturation in Escherichia coli: role of accessory proteins HypA and HypF. J. Bacteriol., 184: 3879-3885.
  91. [73] Kuchenreuther, J. M., Britt, R. D., Swartz, J. R. (2012) New insights into [FeFe] hydrogenase activation and maturase function. PLoS One, 7: e45850.
  92. [13] Bonne, D. R., Whitman, W. B., Rouviere, P., Methanogensis, in Diversity ang taxonomy of methanogens, J.G. Ferry, Editor. 1993: New York and London. p. 35.
  93. [68] Theodorator, E., Huber, R., Böck, A. (2005) [NiFe]-Hydrogenase maturation endopeptidase: structure and function. Biochem. Soc. Trans., 33: 108-111.
  94. [134] Burgdorf, T., Lenz, O., Buhrke, T., Linden, E., Jones, A. K., Albracht, S. P., Friedrich, B. (2005) [NiFe]-hydrogenases of Ralstonia eutropha H16: modular enzymes for oxygen-tolerant biological hydrogen oxidation. J. Mol. Microbiol. Biotechnol., 10: 181-96.
  95. [10] Ettwig, K. F., Butler, M. K., Le Paslier, D., Pelletier, E., Mangenot, S., Kuypers, M. M., Schreiber, F., Dutilh, B. E., Zedelius, J., de Beer, D., Gloerich, J., Wessels, H. J., van Alen, T., Luesken, F., Wu, M. L., van de Pas-Schoonen, K. T., Op den Camp, H. J., Janssen-Megens, E. M., Francoijs, K. J., Stunnenberg, H., Weissenbach, J., Jetten, M. S., Strous, M. (2010) Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature, 464: 543-548.
  96. [57] Vignais, P. M., Billoud, B. (2007) Occurrence classification and biological function of hydrogenases: an overview. Chem. Rev., 107: 4206-4272.
  97. [29] Klein, A. R., Thauer, R. K. (1997) Overexpression of the coenzyme-F420- dependent N5,N10-methylenetetrahydromethanopterin dehydrogenase gene from the hyperthermophilic Methanopyrus kandleri. Eur. J. Biochem., 245: 386- 391.
  98. [26] Vaupel, M., Vorholt, J. A., Thauer, R. K. (1998) Overproduction and one-step purification of the N5,N10-methenyltetrahydromethanopterin cyclohydrolase (Mch) from the hyperthermophilic Methanopyrus kandleri. Extremophiles, 2: 15- 22.
  99. [113] Winn, M. D., Ballard, C. C., Cowtan, K. D., Dodson, E. J., Emsley, P., Evans, P. R., Keegan, R. M., Krissinel, E. B., Leslie, A. G., McCoy, A., McNicholas, S. J., Murshudov, G. N., Pannu, N. S., Potterton, E. A., Powell, H. R., Read, R. J., Vagin, A., Wilson, K. S. (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr D, 67: 235-242.
  100. [114] Afonine, P. V., Grosse-Kunstleve, R. W., Chen, V. B., Headd, J. J., Moriarty, N. W., Richardson, J. S., Richardson, D. C., Urzhumtsev, A., Zwart, P. H., Adams, P. D. (2010) phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. J. Appl. Crystallogr., 43: 669-676.
  101. [130] Lie, T. J., Costa, K. C., Pak, D., Sakesan, V., Leigh, J. A. (2013) Phenotypic evidence that the function of the [Fe]-hydrogenase Hmd in Methanococcus maripaludis requires seven hcg (hmd co-occurring genes) but not hmdII. FEMS Microbiol. Lett., 343: 156-160.
  102. [46] Naumann, E., Fahlbusch, K., Gottschalk, G. (1984) Presence of a trimethylamine HS-coenzyme M methyltransferase in Methanosarcina barkeri. Arch. Microbiol., 138: 79-83.
  103. [25] Vaupel, M., Dietz, H., Linder, D., Thauer, R. K. (1996) Primary structure of cyclohydrolase (Mch) from Methanobacterium thermoautotrophicum (strain Marburg) and functional expression of the mch gene in Escherichia coli. Eur. J. Biochem., 236: 294-300.
  104. [101] Fujishiro, T., Kahnt, J., Ermler, U., Shima, S. (2015) Protein-pyridinol thioester precursor for biosynthesis of the organometallic acyl-iron ligand in [Fe]- hydrogenase cofactor. Nat. Commun., 6: 6895.
  105. [75] Broderick, J. B., Duffus, B. R., Duschene, K. S., Shepard, E. M. (2014) Radical S-adenosylmethionine enzymes. Chem. Rev., 114: 4229-4317.
  106. [127] Shima, S., Chen, D., Xu, T., Wodrich, M. D., Fujishiro, T., Schultz, K. M., Kahnt, J., Ataka, K., Hu, X. (2015) Reconstitution of [Fe]-hydrogenase using model complexes. Nat. Chem., 7: 995-1002.
  107. [85] Afting, C., Kremmer, E., Brucker, C., Hochheimer, A., Thauer, R. K. (2000) Regulation of the synthesis of H2-forming methylenetetrahydromethanopterin dehydrogenase (Hmd) and of HmdII and HmdIII in Methanothermobacter marburgensis. Arch. Microbiol., 174: 225-232.
  108. [66] Olson, J. W., Mehta, N. S., Maier, R. J. (2001) Requirement of nickel metabolism proteins HypA and HypB for full activitz of both hydrogenase and urease in Helicobacter pzlori. Mol. Microbiol., 39: 176-182.
  109. [126] Struck, A. W., Thompson, M. L., Wong, L. S., Micklefield, J. (2012) S-adenosylmethionine-dependent methyltransferases: highly versatile enzymes in biocatalysis, biosynthesis and other biotechnological applications. Chembiochem, 13: 2642-2655.
  110. [60] Watanabe, S., Sasaki, D., Tominaga, T., Miki, K. (2012) Structural basis of [NiFe] hydrogenase maturation by Hyp proteins. Biol. Chem., 393: 1089-1100.
  111. [28] Ceh, K., Demmer, U., Warkentin, E., Moll, J., Thauer, R. K., Shima, S., Ermler, U. (2009) Structural basis of the hydride transfer mechanism in F420-dependent methylenetetrahydromethanopterin dehydrogenase. Biochemistry, 48: 10098- 10105.
  112. [88] Shima, S., Ermler, U. (2011) Structure and function of [Fe]-hydrogenase and its iron-guanylylpyridinol (FeGP) cofactor. Eur. J. Inorg. Chem., 2011: 963-972.
  113. [123] Chen, S. C., Huang, C. H., Lai, S. J., Liu, J. S., Fu, P. K., Tseng, S. T., Yang, C. S., Lai, M. C., Ko, T. P., Chen, Y. (2015) Structure and mechanism of an antibiotics-synthesizing 3-hydroxykynurenine C-methyltransferase. Sci. Rep., 5: 10100.
  114. [122] Zou, X. W., Liu, Y. C., Hsu, N. S., Huang, C. J., Lyu, S. Y., Chan, H. C., Chang, C. Y., Yeh, H. W., Lin, K. H., Wu, C. J., Tsai, M. D., Li, T. L. (2014) Structure and mechanism of a nonhaem-iron SAM-dependent C-methyltransferase and its engineering to a hydratase and an O-methyltransferase. Acta Crystallogr D, 70: 1549-1560.
  115. [119] Köksal, M., Chou, W. K., Cane, D. E., Christianson, D. W. (2012) Structure of geranyl diphosphate C-methyltransferase from Streptomyces coelicolor and implications for the mechanism of isoprenoid modification. Biochemistry, 51: 3003-3010.
  116. [84] Shepard, E. M., McGlynn, S. E., Bueling, A. L., Grady-Smith, C. S., George, S. J., Winslow, M. A., Cramer, S. P., Peters, J. W., Broderick, J. B. (2010) Synthesis of the 2Fe subcluster of the [FeFe]-hydrogenase H cluster on the HydF scaffold. Proc. Natl. Acad. Sci. USA, 107: 10448-10453.
  117. [61] Reissmann, S., Hochleitner, E. Wang, H., Paschos, A., Lottspeich, F., Glass, R. S., Böck, A. (2003) Taming of a poison: biosynthesis of the NiFe-hydrogenase cyanide ligands. Science, 299: 1067-1070.
  118. [21] Vorholt, J. A., Thauer, R. K. (1997) The active species of 'CO2' utilized by formylmethanofuran dehydrogenase from methanogenic Archaea. Eur. J. Biochem., 248: 919-924.
  119. [92] Shima, S., Lyon, E. J., Sordel-Klippert, M., Kauss, M., Kahnt, J., Thauer, R. K., Steinbach, K., Xie, X., Verdier, L., Griesinger, C. (2004) The cofactor of the ironsulfur cluster free hydrogenase hmd: structure of the light-inactivation product. Angew. Chem. Int. Ed., 43: 2547-2551.
  120. [65] Blokesch, M., Albracht, S. P., Matzanke, B. F., Drapal, N. M., Jacobi, A., Bock, A. (2004) The complex between hydrogenase-maturation proteins HypC and HypD is an intermediate in the supply of cyanide to the active site iron of [NiFe]- hydrogenases. J. Mol. Biol., 344: 155-167.
  121. [49] Pisa, K. Y., Weidner, C., Maischak, H., Kavermann, H., Muller, V. (2007) The coupling ion in the methanoarchaeal ATP synthases: H+ vs. Na+ in the A1Ao ATP synthase from the archaeon Methanosarcina mazei Gö1. FEMS Microbiol. Lett., 277: 56-63.
  122. [90] Hiromoto, T., Ataka, K., Pilak, O., Vogt, S., Stagni, M. S., Meyer-Klaucke, W., Warkentin, E., Thauer, R. K., Shima, S., Ermler, U. (2009) The crystal structure of C176A mutated [Fe]-hydrogenase suggests an acyl-iron ligation in the active site iron complex. FEBS Lett., 583: 585-590.
  123. [87] Shima, S., Pilak, O., Vogt, S., Schick, M., Stagni, M. S., Meyer-Klaucke, W., Warkentin, E., Thauer, R. K., Ermler, U. (2008) The Crystal structure of [Fe]- hydrogenase reveals the geometry of the active site. Science, 321: 572-575.
  124. [89] Pilak, O., Mamat, B., Vogt, S., Hagemeier, C. H., Thauer, R. K., Shima, S., Vonrhein, C., Warkentin, E., Ermler, U. (2006) The crystal structure of the apoenzyme of the iron-sulphur cluster-free hydrogenase. J. Mol. Biol., 358: 798- 809.
  125. [117] Dominissini, D., Nachtergaele, S., Moshitch-Moshkovitz, S., Peer, E., Kol, N., Ben-Haim, M. S., Dai, Q., Di Segni, A., Salmon-Divon, M., Clark, W. C., Zheng, G., Pan, T., Solomon, O., Eyal, E., Hershkovitz, V., Han, D., Dore, L. C., Amariglio, N., Rechavi, G., He, C. (2016) The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA. Nature, 530: 441-446.
  126. [71] Brazzolotto, X., Rubach, J. K., Gaillard, J., Gambarelli, S., Atta, M., Fontecave, M. (2006) The [Fe-Fe]-hydrogenase maturation protein HydF from Thermotoga maritima is a GTPase with an iron-sulfur cluster. J. Biol. Chem., 281: 769-774.
  127. [120] Foster, P. G., Nunes, C. R., Greene, P., Moustakas, D., Stround, R. M. (2003) The first structure of an RNA m5C methylatransferase, Fmu, provides insight into catalytic mechanism and specific binding of RNA substrate. Structure, 11: 1609-1620.
  128. [1] Wahlen, M. (1993) The global methane cycle. Annu. Rev. Earth Pl. Sci., 21: 407-426.
  129. [4] Conrad, R. (2009) The global methane cycle: recent advances in understanding the microbial processes involved. Environ. Microbiol. Rep., 1: 285-292.
  130. [2] Ramanathan, V. (1988) The greenhouse theory of climate change: a test by an inadertent global experiment. Science 240: 293-299.
  131. [37] Hedderich, R., Koch, J., Linder, D., Thauer, R. K. (1994) The heterodisulfide reductase from Methanobacterium thermoautotrophicum contains sequence motifs characteristic of pyridine-nucleotide-dependent thioredoxin reductases. Eur. J. Biochem., 225: 253-261.
  132. [78] Kuchenreuther, J. M., Myers, W., Suess, D. L. M., Stich, T. A., Pelmenschikow, V., Schiigi, S. A., Cramer, S. P., Swartz, J. R., Britt, R. D., George, S. J. (2014) The HydG enzyme generates an Fe(CO)2(CN) synthon in assenbly of the FeFe hydrogenase H-cluster. Science, 343: 424-427.
  133. [144] Chandonia, J., Brenner, S. (2006) The impact of structural genomics: expectations and outcomes. Science, 311: 347-351.
  134. [52] Wagner, T., Ermler, U., Shima, S. (2016) The methanogenic CO2 reducing-andfixing enzyme is bifunctional and contains 46 [4Fe-4S] clusters. Science, 354: 114-117.
  135. [34] Gottschalk, G., Thauer, R. K. (2001) The Na+-translocating methyltransferase complex from methanogenic archaea. Biochim. Biophys. Acta, 1505: 28-36.
  136. [146] Jarrett, J. T. (2005) The novel structure and chemistry of iron-sulfur clusters in the adenosylmethionine-dependent radical enzyme biotin synthase. Arch. Biochem. Biophys., 433: 312-321.
  137. [139] Maier, T., Jacobi, A., Sauter, M., Böck (1993) The product of the hypB gene, which is required for nickel incorporation into hydrogenase, is a novel guanine nucleotide-binding protein. J. Bacteriol., 175: 630-635.
  138. [53] Mitchell, P. (1975) The protomotive Q cycle: a Q general formulation. FEBS Lett., 59: 137-139.
  139. [77] Pilet, E., Nicolet, Y., Mathevon, C., Douki, T., Fontecilla-Camps, J. C., Fontecave, M. (2009) The role of the maturase HydG in [FeFe]-hydrogenase active site synthesis and assembly. FEBS Lett., 583: 506-511.
  140. [96] Akiyama, H., Fujisawa, N., Tashiro, Y., Takanabe, N., Sugiyama, A., Tashiro, F. (2003) The role of transcriptional corepressor Nif3l1 in early stage of neural differentiation via cooperation with Trip15/CSN2. J. Biol. Chem., 278: 10752- 10762.
  141. [76] Kriek, M., Martins, F., Challand, M. R., Croft, A., Roach, P. L. (2007) Thiamine biosynthesis in Escherichia coli: identification of the intermediate and by-product derived from tyrosine. Angew. Chem., Int. Ed. Engl., 46: 9223-9226.
  142. [95] Martens, J. A., Genereaux, J., Saleh, A., Brandi, C. J. (1996) Transcriptional activation by Yeast PDR1p Is inhibited by its association with NGG1p/ADA3p. J. Biol. Chem., 271: 15884-15890.
  143. [142] Kuchenreuther, J. M., Stapleton, J. A., Swartz, J. R. (2009) Tyrosine, cysteine, and S-adenosyl methionine stimulate in vitro [FeFe] hydrogenase activation. PLoS One, 4: e7565.
  144. [100] Schulman, B. A., Harper, J. W. (2009) Ubiquitin-like protein activation by E1 enzymes: the apex for downstream signalling pathways. Nat. Rev. Mol. Cell. Biol., 10: 319-331.
  145. [112] Kabsch, W. (2010) XDS. Acta Crystallogr. D, 66: 125-132.
  146. [80] Dinis, P., Suess, D. L. M., Fox, S. J., Harmer, J. E., Driesener, R. C., Paz, L. D. L., Swartz, J. R., Essex, J. W., Britt, R. D., Roach, P. L. (2015) X-ray crystallographic and EPR spectroscopic analysis of HydG, a maturase in [FeFe]-hydrogenase. Proc. Natl. Acad. Sci. USA, 112: 1362-1367.

* Das Dokument ist im Internet frei zugänglich - Hinweise zu den Nutzungsrechten
© UB Marburg 1997 - 2024 Universitätsbibliothek Marburg