On the enzymatic mechanism of 4-hydroxybutyryl-CoA dehydratase and 4-hydroxybutyrate CoA-transferase from Clostridium aminobutyricum

Die 4-Hydroxybutyryl-CoA-Dehydratase aus Clostridium aminobutyricum katalysiert die ungewöhnliche reversible Dehydratisierung von 4-Hydroxybutyryl-CoA zu Crotonyl-CoA. Das Enzym ist im nativen Zustand ein Homotetramer mit einer Masse von 232 kDa, und besteht aus zwei katalytisch aktiven Dimeren mit...

Ausführliche Beschreibung

Gespeichert in:
1. Verfasser: Zhang, Jin
Beteiligte: Buckel, Wolfgang (Prof. Dr.) (BetreuerIn (Doktorarbeit))
Format: Dissertation
Sprache:Englisch
Veröffentlicht: Philipps-Universität Marburg 2010
Biologie
Schlagworte:
Online Zugang:PDF-Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!

1. Laemmli, U. K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4, Nature. 227, 680-685.


2. Decker, K., Jungermann, K. & Thauer, R. K. (1970) Energy production in anaerobic organisms, Angew Chem Int Ed Engl. 9, 138-158.


3. Beinert, H. (2000) Iron-sulfur proteins: ancient structures, still full of surprises, J Biol Inorg Chem. 5, 2-15.


4. Kusukawa, N. & Yura, T. (1988) Heat shock protein GroE of Escherichia coli: key protective roles against thermal stress, Genes Dev. 2, 874-882.


5. Hans, M., Sievers, J., Müller, U., Bill, E., Vorholt, J. A., Linder, D. & Buckel, W. (1999) 2- hydroxyglutaryl-CoA dehydratase from Clostridium symbiosum, Eur J Biochem. 265, 404-414.


6. Berg, I. A., Kockelkorn, D., Buckel, W. & Fuchs, G. (2007) A 3-hydroxypropionate/4- hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea, Science. 318, 1782-1786.


7. Manstein, D. J., Pai, E. F., Schopfer, L. M. & Massey, V. (1986) Absolute stereochemistry of flavins in enzyme-catalyzed reactions, Biochemistry. 25, 6807-6816.


8. Müller, U. & Buckel, W. (1995) Activation of (R)-2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans, Eur J Biochem. 230, 698-704.


9. Bradford, M. M. (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding, Anal Biochem. 72, 248-254.


10. Castanie, M. (1997) A set of pBR322-compatible plasmids allowing the testing of chaperone-assisted folding of proteins overexpressed in Escherichia coli., Anal Biochem. 254, 150-152.


11. Willadsen, P. & Buckel, W. (1990) Assay of 4-hydroxybutyryl-CoA dehydratase from Clostridium aminobutyricum, FEMS Microbiol Lett. 58, 187-191.


12. Buckel, W., Hetzel, M. & Kim, J. (2004) ATP-driven electron transfer in enzymatic radical reactions, Curr Opin Chem Biol. 8, 462-467.


13. Bartsch, R. G. & Barker, H. A. (1961) A vinylacetyl isomerase from Clostridium kluyveri, Arch Biochem Biophys. 92, 122-132.


14. Studium der klinischen Medizin (Bachelor) an der Medizinischen Universtät Xi´an (V. R. China) 08.1999 – 08.2000 Praktikum in dem provinziellen Volksklinikum Shaanxi 08.2000 – 07.2001 Deutsch Intensivkurs an der Philipps-Universität Marburg 10.2001 – 02.2006


15. Kim, J., Darley, D., Selmer, T. & Buckel, W. (2006) Characterization of (R)-2- hydroxyisocaproate dehydrogenase and a family III coenzyme A transferase involved in reduction of L-leucine to isocaproate by Clostridium difficile, Appl Environ Microbiol. 72, 6062- 6069.


16. Werst, M. M., Kennedy, M. C., Houseman, A. L., Beinert, H. & Hoffman, B. M. (1990) Characterization of the [4Fe-4S] + cluster at the active site of aconitase by 57Fe, 33S, and 14N electron nuclear double resonance spectroscopy, Biochemistry. 29, 10533-10540.


17. Geburtsort: Xi´an, V. R. China Familienstand: verheiratet, mit einer Tochter Nationalität: V. R. China Schulbildung und Studium 09.1988 – 07.1994 Gymnasium der Normal Universität Shannxi (V. R.China) 09.1994 – 08.1999


18. Clostridium propionicum. Cloning of gene and identification of glutamate 324 at the active site, Eur J Biochem. 269, 372-380.


19. cluster in the superreduced activator of 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans, J Biol Inorg Chem. 13, 563-574.


20. CoA catalysed by 4-hydroxybutyryl-CoA dehydratase, Chem Commun (Camb), 1210-1.


21. Gruber, K. & Kratky, C. (2002) Coenzyme B 12 dependent glutamate mutase, Curr Opin Chem Biol. 6, 598-603.


22. Ettema, T. J. & Andersson, S. G. (2008) Comment on "A 3-hydroxypropionate/4- hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea", Science. 321, 342; author reply 342.


23. H. (1971) Comments on "the interpretation of the EPR and Mössbauer spectra of two-iron, one- electron iron-sulfur proteins", Biochem Biophys Res Commun. 45, 1119-26.


24. Lichty, J. J., Malecki, J. L., Agnew, H. D., Michelson-Horowitz, D. J. & Tan, S. (2005) Comparison of affinity tags for protein purification, Protein Expr Purif. 41, 98-105.


25. Kim, J., Hetzel, M., Boiangiu, C. D. & Buckel, W. (2004) Dehydration of (R)-2- hydroxyacyl-CoA to enoyl-CoA in the fermentation of alpha-amino acids by anaerobic bacteria, FEMS Microbiol Rev. 28, 455-468.


26. Southern, E. M. (1992) Detection of specific sequences among DNA fragments separated by gel electrophoresis., Biotechnology. 24, 122-139.


27. Barker, H. A., D'Ari, L. & Kahn, J. (1987) Enzymatic reactions in the degradation of 5- aminovalerate by Clostridium aminovalericum, J Biol Chem. 262, 8994-9003. References 126


28. Gerhardt, A., Çinkaya, I., Linder, D., Huisman, G. & Buckel, W. (2000) Fermentation of 4- aminobutyrate by Clostridium aminobutyricum: cloning of two genes involved in the formation and dehydration of 4-hydroxybutyryl-CoA, Arch Microbiol. 174, 189-199.


29. Goloubinoff, P., Diamant, S., Weiss, C. & Azem, A. (1997) GroES binding regulates GroEL chaperonin activity under heat shock, FEBS Lett. 407, 215-219.


30. Wächtershäuser, G. (1992) Groundworks for an evolutionary biochemistry: the iron-sulphur world, Prog Biophys Mol Biol. 58, 85-201.


31. Bothe, H., Darley, D. J., Albracht, S. P., Gerfen, G. J., Golding, B. T. & Buckel, W. (1998) Identification of the 4-glutamyl radical as an intermediate in the carbon skeleton rearrangement catalyzed by coenzyme B 12 -dependent glutamate mutase from Clostridium cochlearium, Biochemistry. 37, 4105-4113.


32. Implications for the mechanism of CoA-ester hydrolysis, J Biol Chem. 274, 20772-20778.


33. Diamant, S., Azem, A., Weiss, C. & Goloubinoff, P. (1995) Increased efficiency of GroE- assisted protein folding by manganese ions, J Biol Chem. 270, 28387-28391.


34. Beinert, H., Holm, R. H. & Munck, E. (1997) Iron-sulfur clusters: nature's modular, multipurpose structures, Science. 277, 653-659.


35. Isolation and sequence of a cDNA encoding the enzyme, J Biol Chem. 267, 7215-7216. 31. Gerhardt, A. (1999) Molekulare Charakterisierung der Schlüsselenzyme des 4- Hydroxybutyrat-Stoffwechsels in Clostridium aminobutyricum: Dehydrogenase, CoA-


36. Wang, B. H. & Biemann, K. (1994) Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of chemically modified oligonucleotides, Anal Chem. 66, 1918-1924.


37. Howard, J. B., Zieske, L., Clarkson, J. & Rathe, L. (1986) Mechanism-based fragmentation of coenzyme A transferase. Comparison of alpha 2-macroglobulin and coenzyme A transferase thiol ester reactions, J Biol Chem. 261, 60-65.


38. Kimura, M. & Yamaguchi, S. (1998) Medium-chain acyl-CoA dehydrogenase deficiency, Ryoikibetsu Shokogun Shirizu, 414-416. References 129


39. Hardman, J. K. & Stadtman, T. C. (1963) Metabolism of amega-amino acids. III. Mechanism of conversion of gamma-aminobutyrate to gamma-hydroxybutryate by Clostridium aminobutyricum, J Biol Chem. 238, 2081-2087.


40. Hardman, J. K. & Stadtman, T. C. (1960) Metabolism of omega-acids. II. Fermentation of delta-aminovaleric acid by Clostridium aminovalericum n. sp, J Bacteriol. 79, 549-552.


41. Hardman, J. K. & Stadtman, T. C. (1960) Metabolism of omega-amino acids. I. Fermentation of gamma-aminobutyric acid by Clostridium aminobutyricum n. sp, J Bacteriol. 79, 544-548.


42. Hardman, J. K. & Stadtman, T. C. (1963) Metabolism of omega-amino acids. IV. gamma Aminobutyrate fermentation by cell-free extracts of Clostridium aminobutyricum, J Biol Chem. 238, 2088-2093.


43. Ben-Zvi, A. P., Chatellier, J., Fersht, A. R. & Goloubinoff, P. (1998) Minimal and optimal mechanisms for GroE-mediated protein folding, Proc Natl Acad Sci U S A. 95, 15275-15280.


44. Fisher, C. L. & Pei, G. K. (1997) Modification of a PCR-based site-directed mutagenesis method, Biotechniques. 23, 570-1, 574.


45. Söhling, B. & Gottschalk, G. (1996) Molecular analysis of the anaerobic succinate degradation pathway in Clostridium kluyveri, J Bacteriol. 178, 871-880.


46. Mössbauer studies of aconitase. Substrate and inhibitor binding, reaction intermediates, and hyperfine interactions of reduced 3Fe and 4Fe clusters, J Biol Chem. 260, 6871-6881.


47. Kiema, T. R., Engel, C. K., Schmitz, W., Filppula, S. A., Wierenga, R. K. & Hiltunen, J. K. (1999) Mutagenic and enzymological studies of the hydratase and isomerase activities of 2- enoyl-CoA hydratase-1, Biochemistry. 38, 2991-2999.


48. Schmidt, T. G. & Skerra, A. (1994) One-step affinity purification of bacterially produced proteins by means of the "Strep tag" and immobilized recombinant core streptavidin, J Chromatogr A. 676, 337-345. References 131


49. Bungert, S., Krafft, B., Schlesinger, R. & Friedrich, T. (1999) One-step purification of the NADH dehydrogenase fragment of the Escherichia coli complex I by means of Strep-tag affinity chromatography, FEBS Lett. 460, 207-211.


50. Selmer, T. & Buckel, W. (1999) Oxygen exchange between acetate and the catalytic glutamate residue in glutaconate CoA-transferase from Acidaminococcus fermentans.


51. & Erlich, H. A. (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase, Science. 239, 487-491.


52. J. & Schleper, C. (2006) Production of recombinant and tagged proteins in the hyperthermophilic archaeon Sulfolobus solfataricus, Appl Environ Microbiol. 72, 102-111. References 133 and reconstitution of glutaconyl-CoA decarboxylase from Acidaminococcus fermentans. Methods Enzymol. 125:547-558


53. Selmer, T., Willanzheimer, A. & Hetzel, M. (2002) Propionate CoA-transferase from


54. Buckel, W. & Golding, B. T. (2006) Radical enzymes in anaerobes, Annu Rev Microbiol. 60, 27-49.


55. Fish, W. W. (1988) Rapid colorimetric micromethod for the quantitation of complexed iron in biological samples, Methods Enzymol. 158, 357-364.


56. He, W.-Z. & Malkin, R. (1994) Reconstitution of iron-sulfur center B of photosystem I damaged by mercuric chloride, Photosynth Res. 41, 381-388.


57. Berthold, C. L., Toyota, C. G., Richards, N. G. & Lindqvist, Y. (2008) Reinvestigation of the catalytic mechanism of formyl-CoA transferase, a class III CoA-transferase, J Biol Chem. 283, 6519-6529.


58. Edmondson, D. E. & Tollin, G. (1983) Semiquinone formation in flavo-and metalloflavoproteins, Top Curr Chem. 108, 109-138.


59. Smith, F. E., Herbert, J., Gaudin, J., Hennessy, D. J. & Reid, G. R. (1984) Serum iron determination using ferene triazine, Clin Biochem. 17, 306-310.


60. Hans, M., Buckel, W. & Bill, E. (2008) Spectroscopic evidence for an all-ferrous [4Fe-4S] 0


61. Manstein, D. J., Massey, V., Ghisla, S. & Pai, E. F. (1988) Stereochemistry and accessibility of prosthetic groups in flavoproteins, Biochemistry. 27, 2300-2305. References 130


62. Scott, R., Näser, U., Friedrich, P., Selmer, T., Buckel, W. & Golding, B. T. (2004) Stereochemistry of hydrogen removal from the 'unactivated' C-3 position of 4-hydroxybutyryl-


63. Robbins, A. H. & Stout, C. D. (1989) Structure of activated aconitase: formation of the [4Fe- 4S] cluster in the crystal, Proc Natl Acad Sci U S A. 86, 3639-3643.


64. Kim, J. J. & Wu, J. (1988) Structure of the medium-chain acyl-CoA dehydrogenase from pig liver mitochondria at 3-A resolution, Proc Natl Acad Sci U S A. 85, 6677-6681.


65. Stickland, L. H. (1935) Studies in the metabolism of the strict anaerobes (genus Clostridium): The oxidation of alanine by C. sporogenes. IV. The reduction of glycine by C. sporogenes, Biochem J. 29, 889-898. References 125


66. Kenealy, W. R. W., D.M. (1985) Studies on the substrate range of Clostridium kluyveri; the use of propanol and succinate, Arch Microbiol. 141, 187-194.


67. Çinkaya, I. (2002) Substrat-induzierte Radikalbildung in dem Eisen-Schwefel-Flavoenzym 4-Hydroxybutyryl-CoA Dehydratase aus Clostridium aminobutyricum, Ph. D. thesis, Philipps Universität Marburg.


68. Fridrich, P. (2008) Substratstereochemie and Untersuchungen zum Mechanismus der 4- Hydroxybutyryl-CoA Dehydratase aus Clostridium aminobutyricum, Doktorarbeit, Philipps Universität Marburg.


69. Scherf, U., Söhling, B., Gottschalk, G., Linder, D. & Buckel, W. (1994) Succinate-ethanol fermentation in Clostridium kluyveri: purification and characterisation of 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA delta 3-delta 2-isomerase, Arch Microbiol. 161, 239-245.


70. Schulman, M. & Wood, H. G. (1975) Succinyl-CoA: propionate CoA-transferase from Propionibacterium shermanii., Methods Enzymol. 35, 235-242. References 132


71. Näser, U., Pierik, A. J., Scott, R., Çinkaya, I. & Buckel, W. (2005) Synthesis of 13 C-labeled gamma-hydroxybutyrates for EPR studies with 4-hydroxybutyryl-CoA dehydratase., Bioorg.


72. Erb, T. J., Berg, I. A., Brecht, V., Müller, M., Fuchs, G. & Alber, B. E. (2007) Synthesis of C 5 -dicarboxylic acids from C 2 -units involving crotonyl-CoA carboxylase/reductase: the ethylmalonyl-CoA pathway, Proc Natl Acad Sci U S A. 104, 10631-10636.


73. Johnson, J. L. & Francis, B. S. (1975) Taxonomy of the Clostridia: ribosomal ribonucleic acid homologies among the species, J Gen Microbiol. 88, 229-244.


74. Friedrich, P., Darley, D. J., Golding, B. T. & Buckel, W. (2008) The complete stereochemistry of the enzymatic dehydration of 4-hydroxybutyryl coenzyme A to crotonyl coenzyme A, Angew Chem Int Ed Engl. 47, 3254-3257.


75. Bornstein, B. T. & Barker, H. A. (1948) The energy metabolism of Clostridium kluyveri and the synthesis of fatty acids, J Biol Chem. 172, 659-669. References 127 References 128


76. Hans, M., Buckel, W. & Bill, E. (2000) The iron-sulfur clusters in 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans. Biochemical and spectroscopic investigations, Eur J Biochem. 267, 7082-7093.


77. Collins, M. D., Lawson, P. A., Willems, A., Cordoba, J. J., Fernandez-Garayzabal, J., Garcia, P., Cai, J., Hippe, H. & Farrow, J. A. (1994) The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations, Int J Syst Bacteriol. 44, 812-826.


78. Buckel, W. (1980) The reversible dehydration of (R)-2-hydroxyglutarate to (E)-glutaconate, Eur. J. Biochem. 106, 439-447.


79. Hashimoto, H., Günther, H. & Simon, H. (1973) The stereochemistry of vinylacetyl-CoA- isomerase of Clostridium kluyveri, FEBS Lett. 33, 81-83.


80. Friedrich, P. (2003) Untersuchungen zur Substrat-Stereochemie der 4-Hydroxybutyryl-CoA Dehydratase und zum Mechanismus der 4-Hydroxybutyrat-CoA-Transferase aus Clostridium aminobutyricum, Diplomarbeit, Philipps Universität Marburg.


81. Engst, S., Vock, P., Wang, M., Kim, J. J. & Ghisla, S. (1999) Mechanism of activation of acyl-CoA substrates by medium chain acyl-CoA dehydrogenase: interaction of the thioester carbonyl with the flavin adenine dinucleotide ribityl side chain, Biochemistry. 38, 257-267.


82. Edmondson, D. & Ghisla, S. (1999) Flavoenzyme structure and function. Approaches using flavin analogues, Methods Mol Biol. 131, 157-179.


83. Ben-Zvi, A., De Los Rios, P., Dietler, G. & Goloubinoff, P. (2004) Active solubilization and refolding of stable protein aggregates by cooperative unfolding action of individual hsp70 chaperones, J Biol Chem. 279, 37298-37303.


84. Hans, M., Bill, E., Cirpus, I., Pierik, A. J., Hetzel, M., Alber, D. & Buckel, W. (2002) Adenosine triphosphate-induced electron transfer in 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans, Biochemistry. 41, 5873-5882.


85. 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.


86. Erb, T. J., Brecht, V., Fuchs, G., Müller, M. & Alber, B. E. (2009) Carboxylation mechanism and stereochemistry of crotonyl-CoA carboxylase/reductase, a carboxylating enoyl-thioester reductase, Proc Natl Acad Sci U S A. 106, 8871-8876.


87. Thomson, A. J. (1983) Iron-sulfur stoichiometry and structure of iron-sulfur clusters in three-iron proteins: evidence for [3Fe-4S] clusters, Proc Natl Acad Sci U S A. 80, 393-396.


88. Kusukawa, N., Yura, T., Ueguchi, C., Akiyama, Y. & Ito, K. (1989) Effects of mutations in heat-shock genes groES and groEL on protein export in Escherichia coli, Embo J. 8, 3517-3521.


89. Wächtershäuser, G. (1990) Evolution of the first metabolic cycles, Proc Natl Acad Sci U S A. 87, 200-204.


90. Hanahan, D. (1983) Studies on transformation of Escherichia coli with plasmids, J Mol Biol. 166, 557-580.