Catalytic mechanism and application of formate dehydrogenase

Biochemistry (Moscow)

Volumn 69, Issue 11, 2004, Pages 1252-1267

  Tishkov, V I ^a   Popov, V O ^b  

^a MOSCOW STATE UNIVERSITY   (Russian Federation)

^b BACH INSTITUTE OF BIOCHEMISTRY   (Russian Federation)

Author keywords

Catalytic mechanism; Chiral synthesis; Cloning; Expression; Pseudomonas sp. 101; Site directed mutagenesis

Indexed keywords

CATALYSIS; CLONING; MICROORGANISMS; PH EFFECTS; PHYSIOLOGY; PLANTS (BOTANY); SUBSTRATES; CARBOXYLIC ACIDS; ENZYMES; MUTAGENESIS;

CATALYTIC MECHANISM; CHIRAL SYNTHESIS; FORMATE DEHYROGENASE (FDH); SITE DIRECTED MUTAGENESIS; CATALYTIC MECHANISMS; EXPRESSION; PSEUDOMONAS SP. 101;

ENZYMES; SYNTHESIS (CHEMICAL);

PSEUDOMONAS; PSEUDOMONAS SP.; PSEUDOMONAS SP. 101;

FORMATE DEHYDROGENASE; METHANE;

AMINO ACID SEQUENCE; CATALYSIS; ENZYMOLOGY; GENETICS; KINETICS; METABOLISM; METHYLOCOCCACEAE; MOLECULAR CLONING; MOLECULAR GENETICS; PLANT; REVIEW; SEQUENCE ALIGNMENT;

AMINO ACID SEQUENCE; CATALYSIS; CLONING, MOLECULAR; FORMATE DEHYDROGENASES; KINETICS; METHANE; METHYLOCOCCACEAE; MOLECULAR SEQUENCE DATA; PLANTS; SEQUENCE ALIGNMENT;

EID: 11144247396     PISSN: 00062979     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10541-005-0071-x     Document Type: Review

References (125)

1. Vinals, C., Depiereux, E., and Feytmans, E. (1993) Biochem. Biophys. Res. Commun., 192, 182-188.
2. Wichmann, R., Wandrey, C., Buckmann, A. F., and Kula, M. R. (1981) Biotechnol. Bioeng., 23, 2789-2802.
3. Hummel, W., and Kula, M. R. (1989) Eur. J. Biochem., 184, 1-13.
4. Zhao, H., and van der Donk, W. A. (2003) Curr. Opin. Biotechnol., 14, 583-589.
5. Bommarius, A. S., Schwarm, M., Stingl, K., Kottenhahn, M., Huthmacher, K., and Drauz, K. (1995) Tetrahedron: Asymmetry, 6, 2851-2888.
6. Popov, V. O., and Lamzin, V. S. (1994) Biochem. J., 301, 625-643.
7. Popov, V. O., and Tishkov, V. I. (2003) in Protein Structures: Kaleidoscope of Structural Properties and Functions (Uversky, V. N., ed.) Research Signpost, Kerala, India, pp. 441-473.
8. Rodionov, Yu. V. (1981) Usp. Mikrobiol., No. 16, 104-138.
9. Khangulov, S. V., Gladyshev, V. N., Dismukes, G. C., and Stadtman, T. C. (1998) Biochemistry, 37, 3518-3528.
10. Hollenberg, C. P., and Janowicz, Z. (1989) Eur. Patent EP1987000110417, Bulletin 89/03.
11. Tishkov, V. I., Galkin, A. G., and Egorov, A. M. (1991) Dokl. Akad. Nauk SSSR, 317, 345-348.
12. Galkin, A., Kulakova, L., Tishkov, V., Esaki, N., and Soda, K. (1995) Appl. Microbiol. Biotechnol., 44, 479-483.
13. Mitsunaga, T., Tanaka, Y., Yoshida, T., and Watanabe, K. (2000) Jap. Patent JP245471A2 of 12.09.2000.
14. Shinoda, T., Satoh, T., Mineki, S., Iida, M., and Taguchi, H. (2002) Biosci. Biotechnol. Biochem., 66, 271-276.
15. Nanba, H., Takaoka, Y., and Hasegawa, J. (2003) Biosci. Biotechnol. Biochem., 67, 720-728.
16. Nanba, H., Takaoka, Y., and Hasegawa, J. (2003) Biosci. Biotechnol. Biochem., 67, 2145-2153.
17. Allen, S. J., and Holbrook, J. J. (1995) Gene, 162, 99-104.
18. Sakai, Y., Murdanoto, A. P., Konishi, T., Iwamatsu, A., and Kato, N. (1997) J. Bacteriol., 179, 4480-4485.
19. Slusarczyk, H., Felber, S., Kula, M. R., and Pohl, M. (2000) Eur. J. Biochem., 267, 1280-1289.
20. Labrou, N. E., and Rigden, D. J. (2001) Biochem. J., 354, 455-463.
21. Goldberg, S. L., Cino, P. M., Patel, R. N., Nanduri, V. B., Johnston, R. M., and Johnston, R. (2004) USA Patent US 2004/0038237 Al of 26.02.2004.
22. Baba, T., Takeuchi, F., Kuroda, M., Yuzawa, H., Aoki, K.-I., Oguchi, A., Nagai, Y., Iwama, N., Asano, K., Naimi, T., Kuroda, H., Cui, L., Yamamoto, K., and Hiramatsu, K. (2002) Lancet, 359, 1819-1827.
23. Parkhill, J., Sebaihia, M., Preston, A., Murphy, L. D., Thomson, N., Harris, D. E., Holden, M. T. G., Churcher, C. M., Bentley, S. D., Mungall, K. L., Cerdeno-Tarraga, A. M., Temple, L., James, K., Harris, B., Quail, M. A., Achtman, M., Atkin, R., Baker, S., Basham, D., Bason, N., Cherevach, I., Chillingworth, T., Collins, M., Cronin, A., Davis, P., Doggett, J., Feltwell, T., Goble, A., Hamlin, N., Hauser, H., Holroyd, S., Jagels, K., Leather, S., Moule, S., Norberczak, H., O'Neil, S., Ormond, D., Price, C., Rabbinowitsch, E., Rutter, S., Sanders, M., Saunders, D., Seeger, K., Sharp, S., Simmonds, M., Skelton, J., Squares, R., Squares, S., Stevens, K., Unwin, L., Whitehead, S., Barrell, B. G., and Maskell, D. J. (2003) Nat. Genet., 35, 32-40.
24. Omura, S., Ikeda, H., Ishikawa, J., Hanamoto, A., Takahashi, C., Shinose, M., Takahashi, Y., Horikawa, H., Nakazawa, H., Osonoe, T., Kikuchi, H., Shiba, T., Sakaki, Y., and Hattori, M. (2001) Proc. Natl. Acad. Sci. USA, 98, 12215-12220.
25. De la Torre, J. R., Christianson, L. M., Beja, O., Suzuki, M. T., Karl, D. M., Heidelberg, J., and De Long, E. F. (2003) Proc. Natl. Acad. Sci. USA, 100, 12830-12835.
26. Beja, O., Aravind, L., Koonin, E. V., Suzuki, M. T., Hadd, A., Nguyen, L. R., Jovanovich, S. B., Gates, C. M., Feldman, R. A., Spudich, J. L., Spudich, E. N., and De Long, E. F. (2000) Science, 289, 1902-1906.
27. Barnett, M. J., Fisher, R. F., Jones, T., Komp, C., Abola, A. R., Barloy-Hubler, F., Bowser, L., Capela, D., Galibert, F., Gouzy, J., Gurjal, M., Hong, A., Huizar, L., Hyman, R. W., Kahn, D., Kahn, M. L., Kalman, S., Keating, D. H., Palm, C., Peck, M. C., Surzycki, R., Wells, D. H., Yeh, K. C., Davis, R. W., Federspiel, N. A., and Long, S. R. (2001) Proc. Natl. Acad. Sci. USA, 98, 9883-9888.
28. Souciet, J. L., Aigle, M., Artiguenave, F., Blandin, G., Bolotin-Fukuhara, M., Bon, E., Brottier, R., Casaregola, S., de-Montigny, J., Dujon, B., Durrens, P., Lepingle, A., Llorente, B., Malpertuy, A., Neuveglise, C., Ozier-Kalogeropoulos, O., Potier, S., Saurin, W., Tekaia, F., Hoffman, C., Wesolowski-Louvel, M., Wincker, R., and Weissenbach, J. (2000) FEBS Lett., 487, 3-12.
29. Ostergaard, S., Olsson, L., and Nielsen, J. (2000) Microbiol. Rev., 64, 34-50.
30. Overkamp, K. M., Kolter, P., van Der, H. R., Schoondermark-Stolk, S., Luttik, M. A. H., van Dijken, J. R., and Pronk, J. T. (2002) Yeast, 19, 509-520.
31. Serov, A. E. (2002) Structure-Function Relationships in Recombinant Formate Dehydrogenases from Baker's Yeast and Methylotrophic Bacteria: Ph.D. Thesis (Chemistry) [in Russian], Lomonosov Moscow State University, Moscow.
32. Serov, A. E., Popova, A. S., and Tishkov, V. I. (2002) Doklady RAN, 382, 401-405.
33. Saleeba, J. A., Cobbett, C. S., and Hynes, M. J. (1992) Mol. Gen. Genet., 235, 349-358.
34. Chow, C. M., and Raj Bhandary, U. L. (1993) J. Bacteriol., 175, 3703-3709.
35. Davison, D. C. (1951) Biochem. J., 49, 520-526.
36. Kanamori, T., and Suzuki, Y. (1968) Enzymologia, 35, 185-197.
37. Peacock, D., and Boulter, D. (1970) Biochem. J., 120, 763-769.
38. Ohyama, T., and Yamazaki, I. (1974) J. Biochem. (Tokyo), 75, 1257-1263.
39. Ohyama, T., and Yamazaki, I. (1975) J. Biochem. (Tokyo), 77, 845-852.
40. Colas des Francs-Small, C., Ambard-Bretteville, F., Darpas, A., Sallantin, M., Huet, J. C., Pernollet, J. C., and Remy, R. (1992) Plant Physiol., 98, 273-278.
41. Colas des Francs-Small, C., Ambard-Bretteville, F., Small, I. D., and Remy, R. (1993) Plant Physiol., 102, 1171-1177.
42. Ambard-Bretteville, F., Small, I., Grandjean, O., and Colas des Francs-Small, C. (2003) Biochem. Biophys. Res. Commun., 311, 966-971.
43. Jansch, L., Kraft, V., Schmilz, U. K., and Braun, H. P. (1996) Plant J., 9, 357-368.
44. Hourton-Cabassa, C., Ambard-Bretteville, F., Moreau, F., de Virville, J. D., Remy, R., and Colas des Francs-Small, C. (1998) Plant Physiol., 116, 627-635.
45. Suzuki, K., Itai, R., Suzuki, K., Nakanishi, H., Nishizawa, N. K., Yoshimura, E., and Mori, S. (1998) Plant Physiol., 116, 725-732.
46. Thompson, P., Bowsher, C. G., and Tobin, A. K. (1998) Plant Physiol., 118, 1089-1099.
47. Ambard-Bretteville, F., Sorin, C., Rebeille, F., Hourton-Cabassa, C., and Colas des Francs-Small, C. (2003) Plant Mol. Biol., 52, 1153-1168.
48. Hanson, A. D., Gage, D. A., and Shachar-Hill, Y. (2000) Trends Plant Sci., 5, 206-213.
49. Kreuzwieser, J., Schnitzler, J. P., and Steinbrecher, R. (1999) Plant Biol., 1, 149-159.
50. Li, R., Ziola, B., and King, J. (2000) J. Plant Physiol., 157, 161-167.
51. Olson, B. J., Skavdahl, M., Ramberg, H., Osterman, J. C., and Markwell, J. (2000) Plant Sci., 159, 205-212.
52. Shiraishi, T., Fukusaki, E., and Kobayashi, A. (2000) J. Biosci. Bioeng., 89, 241-246.
53. Li, R., Bonham-Smith, P. C., and King, J. (2001) Canad. J. Botany-Revue Canadienne de Botanique, 79, 796-804.
54. Herman, P. L., Ramberg, H., Baack, R. D., Markwell, J., and Osterman, J. C. (2002) Plant Sci., 163, 1137-1145.
55. Li, R., Moore, M., and King, J. (2003) Plant Cell Physiol., 44, 233-241.
56. Nakai, K., and Kanehisa, M. (1992) Genomics, 14, 897-911.
57. Emannuelsson, O., Nielsen, H., and von Heijne, G. (1999). Protein Sci., 8, 978-984.
58. Baack, R. D., Markwell, J., Herman, P. L., and Osterman, J. C. (2003) J. Plant Physiol., 160, 445-450.
59. Weerasinghe, P. A., Weerasekera, M. L. M. C., and van Holm, L. H. J. (1999) Biologia Plantarum, 42, 541-547.
60. Bykova, N. V., Egsgaard, H., and Moller, I. M. (2003) FEBS Lett., 540, 141-146.
61. Bykova, N. V., Stensballe, A., Egsgaard, H., Jensen, O. N., and Moller, I. M. (2003) J. Biol. Chem., 278, 26021-26030.
62. Fedorchuk, V. V., Galkin, A. G., Yasnyi, I. E., Kulakova, L. B., Rojkova, A. M., Filippova, A. A., and Tishkov, V. I. (2002) Biochemistry (Moscow), 67, 1145-1151.
63. Gul-Karaguler, N., Sessions, R. B., Clarke, A. R., and Holbrook, J. (2001) Biotechnol. Lett., 23, 283-287.
64. Serov, A. E., Popova, A. S., Fedorchuk, V. V., and Tishkov, V. I. (2002) Biochem. J., 367, 841-847.
65. Lamzin, V. S., Dauter, Z., Popov, V. O., Harutyunyan, E. H., and Wilson, K. S. (1994) J. Mol. Biol., 236, 759-785.
66. Shannon, C. E. (1997) MD Comput., 14, 306-317 (reprinting of the paper The Mathematical Theory of Communication (1963)).
67. Shannon, C. E. (1997) MD Comput., 14, 306-317 (reprinting of the paper The Mathematical Theory of Communication (1963)).
68. Wilson, A. G. (1970) Entropy in Urban and Regional Modelling, Pion Limited, London.
69. Sander, C., and Schneider, R. (1991) Proteins, 9, 56-68.
70. Tishkov, V. I., Matorin, A. D., Rojkova, A. M., Fedorchuk, V. V., Savitsky, P. A., Dementieva, L. A., Lamzin, V. S., Mezentzev, A. V., and Popov, V. O. (1996) FEBS Lett., 390, 104-108.
71. Iida, M., Kitamura-Kimura, K., Maeda, H., and Mineki, S. (1992) Biosci. Biotechnol. Biochem., 56, 1966-1970.
72. Tishkov, V. I., Galkin, A. G., Gladyshev, V. N., Karzanov, V. V., and Egorov, A. M. (1992) Biotekhnologiya, No. 5, 52-59.
73. Mezentsev, A. V., Ustinnikova, T. B., Tikhonova, T. V., and Popov, V. O. (1996) Prikl. Biokhim. Mikrobiol, 32, 589-595.
74. Slusarczyk, H., Felber, S., Kula, M.-R., and Pohl, M. (2003) Eur. Patent EP1295937-A2N of 26.03.2003.
75. Popov, V. O., Shumilin, I. A., Ustinnikova, T. B., Lamzin, V. S., and Egorov, Ts. A. (1990) Bioorg. Khim., 16, 324-335.
76. Tishkov, V. I. (2002) Bull. Moscow Univ., Ser. 2, Chemistry, 43, 380-387.
77. Blanchard, J. S., and Cleland, W. W. (1980) Biochemistry, 19, 3543-3550.
78. Hermes, J. D., Morrical, S. W., O'Leary, M. H., and Cleland, W. W. (1984) Biochemistry, 23, 5479-5488.
79. Tishkov, V. I., Galkin, A. G., and Egorov, A. M. (1989) Biokhimiya, 54, 299-305.
80. Popov, V. O., Egorov, A. M., and Berezin, I. V. (1978) Dokl. Akad. Nauk SSSR, 240, 217-220.
81. Tishkov, V. I., Galkin, A. G., and Egorov, A. M. (1989) Biochimie, 71, 551-557.
82. Bocanegra, J. A., Scrutton, N. S., and Perham, R. N. (1993) Biochemistry, 32, 2737-2740.
83. Chen, Z., Lee, W. R., and Chang, S. H. (1991) Eur. J. Biochem., 202, 263-267.
84. Chen, Z., Tsigelny, I., Lee, W. R., Baker, M. E., and Chang, S. H. (1994) FEBS Lett., 356, 81-85.
85. Chen, R., Greer, A., and Dean, A. M. (1996) Proc. Natl. Acad. Sci. USA, 93, 12171-12176.
86. Tishkov, V. I., Galkin, A. G., and Egorov, A. M. (1993) Proc. Int. Conf. "Enzyme Engineering XII", Deu Ville, France, p. 54.
87. Shutte, H., Flossdorf, J., Sahm, H., and Kula, M.-R. (1976) Eur. J. Biochem., 62, 151-160.
88. Popov, V. O., Rodionov, Yu. V., Egorov, A. M., and Berezin, I. V. (1978) Bioorg. Khim., 4, 117-129.
89. La Reau, R. D., and Anderson, V. E. (1989) J. Biol. Chem., 264, 15338-15343.
90. Weinhold, E. G., Glasfeld, A., Ellington, A. D., and Benner, S. A. (1991) Proc. Natl. Acad. Sci. USA, 88, 8420-8424.
91. Shaked, Z., and Whitesides, G. M. (1980) J. Am. Chem. Soc., 102, 7104-7105.
92. Mesentsev, A. V., Lamzin, V. S., Tishkov, V. I., Ustinnikova, T. B., and Popov, V. O. (1997) Biochem. J., 321, 475-480.
93. Neuhauser, W., Steininger, M., Haltrich, D., Kulbe, K. D., and Nidetzky, B. (1998) Biotechnol. Bioeng., 60, 277-282.
94. Berezin, I. V., Tishkov, V. I., Karzanov, V. V., Avilova, T. V., Egorov, A. M., Petkyavichene, R. I., Vaitkyavichus, R.-K., and Glemzha, A. A. (1989) USSR Patent, No. 1479513, Byul. Izobret. (1989) No. 18.
95. Berezin, I. V., Tishkov, V. I., Karzanov, V. V., Avilova, T. V., Egorov, A. M., Petkyavichene, R. I., Vaitkyavichus, R.-K., and Glemzha, A. A. (1989) USSR Patent, No. 1479513, Byul. Izobret. (1989) No. 18.
96. Weusterbotz, D., and Wandrey, C. (1995) Proc. Biochem., 30, 563-571.
97. Labrou, N. E., Rigden, D. J., and Clonis, Y. D. (2000) Eur. J. Biochem., 267, 6657-6664.
98. Seelbach, K., Riebel, B., Hummel, W., Kula, M. R., Tishkov, V. I., Egorov, A. M., Wandrey, C., and Kragl, U. (1996) Tetrahedron Lett., 37, 1377-1380.
99. Weuster-Botz, D., Paschold, H., Striegel, B., Gieren, H., Kula, M.-R., and Wandrey, C. (1994) Chem. Eng. Technol., 17, 131-137.
100. Rodionov, Yu. V., Avilova, T. V., and Popov, V. O. (1977) Biokhimiya, 42, 2020-2026.
101. Tishkov, V. I., Galkin, A. G., Marchenko, G. N., Egorova, O. A., Sheluho, D. V., Kulakova, L. B., Dementieva, L. A., and Egorov, A. M. (1993) Biochem. Biophys. Res. Commun., 192, 976-981.
102. Odintseva, E. R., Popova, A. S., Rojkova, A. M., and Tishkov, V. I. (2002) Bull. Moscow Univ., Ser. 2, Chemistry, 43, 356-359.
103. Mitsuhashi, K., Yamamoto, H., and Kimoto, N. (2001) Eur. Patent EP1211316-A of 27.11.2001.
104. Rojkova, A. M., Galkin, A. G., Kulakova, L. B., Serov, A. E., Savitsky, P. A., Fedorchuk, V. V., and Tishkov, V. I. (1999) FEBS Lett., 445, 183-188.
105. Serov, A. E., and Tishkov, V. I. (2002) Bull. Moscow Univ., Ser. 2, Chemistry, 43, 345-349.
106. Serov, A. E., Odintseva, E. R., Uporov, I. V., and Tishkov, V. I. (2005) Biochemistry (Moscow), in press.
107. Tishkov, V. I., Galkin, A. G., Fedorchuk, V. V., Savitsky, P. A., Rojkova, A. M., Gieren, H., and Kula, M. R. (1999) Biotechnol. Bioeng., 64, 187-193.
108. Reichert, U., Knieps, E., Slusarczyk, H., Kula, M. R., and Thommes, J. (2001) J. Biochem. Biophys. Meth., 49, 533-552.
109. Leonida, M. (2001) Curr. Med. Chem., 8, 345-369.
110. Bornscheuer, U. T., and Pohl, M. (2001) Curr. Opin. Chem. Biol., 5, 137-143.
111. Hummel, W. (1999) Trends Biotechnol., 17, 487-492.
112. Kragl, U., Kruse, W., Hummel, W., and Wandrey, C. (1996) Biotechnol. Bioeng., 52, 309-319.
113. Liese, A., and Filho, M. V. (1999) Curr. Opin. Biotechnol., 10, 595-603.
114. Patel, R. N. (2000) Adv. Appl. Microbiol., 47, 33-78.
115. Carrea, G., and Ottolina, G. (2002) Biocatal. Biotransf., 18, 119-132.
116. Kragl, U., VasicRacki, D., and Wandrey, C. (1996) Bioproc. Eng., 14, 291-297.
117. Seelbach, K., and Kragl, U. (1997) Enzyme Microb. Technol., 20, 389-392.
118. Rissom, S., Schwarz-Linek, U., Vogel, M., Tishkov, V. I., and Kragl, U. (1997) Tetrahedron: Asymmetry, 8, 2523-2526.
119. Liese, A., Zelinski, T., Kula, M. R., Kierkels, H., Karutz, M., Kragl, U., and Wandrey, C. (1998) J. Mol. Catal. B-Enzymatic,4, 91-99.
120. Orlich, B., Berger, H., Lade, M., and Schomacker, R. (2000) Biotechnol. Bioeng., 70, 638-646.
121. Zelinski, T., Liese, A., Wandrey, C., and Kula, M. R. (1999) Tetrahedron: Asymmetry, 10, 1681-1687.
122. Galkin, A., Kulakova, L., Yoshimura, T., Soda, K., and Esaki, N. (1997) Appl. Environ. Microbiol., 63, 4651-4656.
123. Takeshita, K., Ishida, Y., Takada, G., and Izumori, K. (2000) J. Biosci. Bioeng., 90, 545-548.
124. Galkin, A., Kulakova, L., Yamamoto, H., Tanizawa, K., Tanaka, Y., Esaki, N., and Soda, K. (1997) J. Ferment. Bioeng., 83, 299-300.
125. Schwarz-Linek, U., Krodel, A., Ludwig, F. A., Schulze, A., Rissom, S., Kragl, U., Tishkov, V. I., and Vogel, M. (2001) Synthesis-Stuttgart, 33, 947-951.