Mechanism of the tyrosine ammonia lyase reaction-tandem nucleophilic and electrophilic enhancement by a proton transfer

Chemistry - A European Journal

Volumn 18, Issue 25, 2012, Pages 7793-7802

  Pilbák, Sarolta ^a   Farkas, Ödön ^b   Poppe, László ^a  

^a BUDAPEST UNIVERSITY OF TECHNOLOGY AND ECONOMICS   (Hungary)

^b EÖTVÖS LORÁND UNIVERSITY   (Hungary)

Author keywords

Conformation analysis; Density functional calculations; Enzyme catalysis; Lyases; Reaction mechanisms

Indexed keywords

3D STRUCTURE; AMINO ACID SEQUENCE; AMMONIA LYASE; BOND-BREAKING; CONFORMATION ANALYSIS; ELECTROPHILIC ACTIVATION; ENZYME CATALYSIS; FRIEDEL-CRAFTS; HIGH ENERGY; L-TYROSINE; LYASES; NUCLEOPHILIC ACTIVATION; REACTION MECHANISM; TRANSITION STATE;

AMMONIA; DENSITY FUNCTIONAL THEORY; ENZYMES; MOLECULAR MODELING; PROTON TRANSFER;

AMINO ACIDS;

AMMONIA LYASE; IMIDAZOLE DERIVATIVE; L TYROSINE AMMONIA LYASE; L-TYROSINE AMMONIA-LYASE; PROTON;

ARABIDOPSIS; ARTICLE; CATALYSIS; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; ENZYMOLOGY; GENETICS; METABOLISM; MOLECULAR GENETICS; RHODOBACTER SPHAEROIDES;

AMMONIA-LYASES; ARABIDOPSIS; CATALYSIS; IMIDAZOLES; MODELS, CHEMICAL; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; PROTONS; RHODOBACTER SPHAEROIDES;

EID: 84862622367     PISSN: 09476539     EISSN: 15213765     Source Type: Journal    
DOI: 10.1002/chem.201103662     Document Type: Article

References (68)

1. J. A. Kyndt, T. E. Meyer, M. A. Cusanovich, J. J. Van Beeumen, FEBS Lett. 2002, 512, 240-244.
2. D. S. Hodgins, J. Biol. Chem. 1971, 246, 2977-2985.
3. a) L. Givot, T. A. Smith, R. H. Abeles, J. Biol. Chem. 1969, 244, 6341-6353
4. b) R. B. Wickner, J. Biol. Chem. 1969, 244, 6550-6552.
5. a) B. Langer, M. Langer, J. R-Tey, Adv. Protein Chem. 2001, 58, 175-214
6. b) L. Poppe, J. R-Tey, Angew. Chem. 2005, 117, 3734-3754
7. Angew. Chem. Int. Ed. 2005, 44, 3668-3688.
8. T. F. Schwede, J. R-Tey, G. E. Schulz, Biochemistry 1999, 38, 5355-5361.
9. a) L. Poppe, Curr. Opin. Chem. Biol. 2001, 5, 512-524
10. b) J. R-Tey, Biochim. Biophys. Acta 2003, 1647, 179-184.
11. J. C. Calabrese, D. B. Jordan, A. Boodhoo, S. Sariaslani, T. Vannelli, Biochemistry 2004, 43, 11403-11416.
12. L. Wang, A. Gamez, C. N. Sarkissian, M. Straub, M. G. Patch, G. W. Han, S. Striepeke, P. Fitzpatrick, C. R. Scriver, R. C. Stevens, Mol. Genet. Metab. 2005, 86, 134-140.
13. H. Ritter, G. E. Schulz, Plant Cell 2004, 16, 3426-3436.
14. M. C. Moffitt, G. V. Louie, M. E. Bowman, J. Pence, J. P. Noel, B. S. Moore, Biochemistry 2007, 46, 1004-1012.
15. L. Wang, A. Gamez, H. Archer, E. E. Abola, C. N. Sarkissian, P. Fitzpatrick, D. Wendt, Y. Zhang, M. Vellard, J. Bliesath, S. M. Bell, J. F. Lemontt, C. R. Scriver, R. C. Stevens, J. Mol. Biol. 2008, 380, 623-635.
16. G. V. Louie, M. E. Bowman, M. C. Moffitt, T. J. Baiga, B. S. Moore, J. P. Noel, Chem. Biol. 2006, 13, 1327-1338.
17. a) K. D. Walker, K. Klettke, T. Akiyama, R. Croteau, J. Biol. Chem. 2004, 279, 53947-53954
18. b) C. L. Steele, Y. Chen, B. A. Dougherty, W. Li, S. Hofstead, K. S. Lam, Z. Xing, S. J. Chiang, Arch. Biochem. Biophys. 2005, 438, 1-10
19. c) W. Mutatu, K. L. Klettke, C. Foster, K. D. Walker, Biochemistry 2007, 46, 9785-9794.
20. L. Feng, U. Wanninayake, S. Strom, J. Geiger, K. D. Walker, Biochemistry 2011, 50, 2919-2930.
21. a) S. D. Christenson, W. Liu, M. D. Toney, B. Shen, J. Am. Chem. Soc. 2003, 125, 6062-6063
22. b) C. V. Christianson, T. J. Montavon, S. G. Van Lanen, B. Shen, S. D. Bruner, Biochemistry 2007, 46, 7205-7214.
23. H. A. Cooke, C. V. Christianson, S. D. Bruner, Curr. Opin. Chem. Biol. 2009, 13, 460-468.
24. a) L. Poppe, J. R-Tey, Curr. Org. Chem. 2003, 7, 1297-1315
25. b) N. J. Turner, Curr. Opin. Chem. Biol. 2011, 15, 234-240
26. c) L. Poppe, C. Paizs, K. Kov-cs, F.-D. Irimie, B. V-rtessy in Unnatural Amino Acids: Methods and Protocols Series: Methods in Molecular Biology, Vol. 794 (Eds.: L. Pollegioni, S. Servi), Humana Press, New York, 2012, pp. 3-19.
27. a) H. Tanaka, T. Oudou, K. Uchida, Jap. 63148992, 1988
28. b)G. Renard, J. C. Guilleux, C. Bore, V. Malta-Valette, D. A. Lerner, Biotechnol. Lett. 1992, 14, 673-678
29. c) A. Gloge, B. Langer, L. Poppe, J. R-Tey, Arch. Biochem. Biophys. 1998, 359, 1-7
30. d)W. Liu, US 5981239, 1999
31. e) A. Gloge, J. Zon A. Kovri, J. Rtey, Chem. Eur. J. 2000, 6, 3386-3390
32. f) C. Paizs, A. Katona, J. R-Tey, Chem. Eur. J. 2006, 12, 2739-2744
33. g) C. Paizs, A. Katona, J. Rtey, Eur. J. Org. Chem. 2006, 1113-1116
34. h) C. Paizs, M. I. Toşa, L. C. Bencze, J. Brem, F.-D. Irimie, J. Rtey, Heterocycles 2011, 82, 1217-1228.
35. D. Rother, L. Poppe, S. Viergutz, B. Langer, J. R-Tey, Eur. J. Biochem. 2001, 268, 6011-6019.
36. D. Rother, L. Poppe, G. Morlock, S. Viergutz, J. R-Tey, Eur. J. Biochem. 2002, 269, 3065-3075.
37. T. A. Smith, F. H. Cordelle, R. H. Abeles, Arch. Biochem. Biophys. 1967, 120, 724-725.
38. K. R. Hanson, E. A. Havir, Arch. Biochem. Biophys. 1970, 141, 1-17.
39. J. D. Hermes, P. M. Weiss, W. W. Cleland, Biochemistry 1985, 24, 2959-2967.
40. M. Langer, A. Pauling, J. R-Tey, Angew. Chem. 1995, 107, 1585-1587
41. Angew. Chem. Int. Ed. Engl. 1995, 34, 1464-1465.
42. P. A. Frey, A. D. Hegeman, Enzymatic Reaction Mechanisms, Oxford University Press, Oxford, 2007, pp. 456-461.
43. S. Bartsch, U. T. Bornscheuer, Angew. Chem. 2009, 121, 3412-3415
44. Angew. Chem. Int. Ed. 2009, 48, 3362-3365.
45. K. T. Watts, B. N. Mijts, P. C. Lee, A. J. Manning, C. Schmidt-Dannert, Chem. Biol. 2006, 13, 1317-1326.
46. M. Baedeker, G. E. Schulz, Eur. J. Biochem. 2002, 269, 1790-1797.
47. M. Baedeker, G. E. Schulz, Structure 2002, 10, 61-67.
48. S. Pilbak, A. Tomin, J. R-Tey, L. Poppe, FEBS J. 2006, 273, 1004-1019.
49. A. L. Seff, S. Pilb-k, I. Silaghi-Dumitrescu, L. Poppe, J. Mol. Model. 2011, 17, 1551-1563.
50. C. V. Christianson, T. J. Montavon, G. M. Festin, H. A. Cooke, B. Shen, S. D. Bruner, J. Am. Chem. Soc. 2007, 129, 15744-15745.
51. T. J. Montavon, C. V. Christianson, G. M. Festin, B. Shen, S. D. Bruner, Bioorg. Med. Chem. Lett. 2008, 18, 3099-3102.
52. M. Luić, Z. Stefanić, I. Ceilinger, M. Hodošč ek, D. Janežič, T. Lenac, A. Leščić, D. Šepac, S. Tomić, J. Phys. Chem. B. 2008, 112, 4876-4883.
53. A. C. Schroeder, S. Kumaran, L. M. Hicks, R. E. Cahoon, C. Halls, O. Yu, P. M. Jez, Phytochemistry 2008, 69, 1496-1506.
54. A. Peterkofsky, J. Biol. Chem. 1962, 237, 787-795.
55. C. V. Christenson, W. Wu, M. A. Spies, B. Shen, M. D. Toney, Biochemistry 2003, 42, 12708-12718.
56. M. M. Heberling, Personal Communication 2011.
57. M. Lundberg, T. Kawatsu, T. Vreven, M. J. Frisch, K. Morokuma, J. Chem. Theory Comput. 2009, 5, 222-234.
58. K. R. Hanson, Arch. Biochem. Biophys. 1981, 211, 575-588.
59. R. Karaman, Tetrahedron Lett. 2009, 50, 7304-7309.
60. Hyperchem 7.5, Hypercube, Inc., 2003.
61. Gaussian 03, Revision E.01, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, J. A. Montgom-ery, Jr., T. Vreven, K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala, K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg, V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain, O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford, J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, J. A. Pople, Gaussian, Inc., Wallingford CT, 2004.
62. A. D. Becke, J. Chem. Phys. 1993, 98, 5648-5652.
63. C. Lee, W. Yang, R. G. Parr, Phys. Rev. B 1988, 37, 785-789.
64. A. K. Rappe, C. J. Casewit, K. S. Colwell, W. A. Goddard III, W. M. Skiff, J. Am. Chem. Soc. 1992, 114, 10024-10035.
65. T. Vreven, K. Morokuma, O. Farkas, H. B. Schlegel, M. J. Frisch, J. Comput. Chem. 2003, 24, 760-769.
66. H. B. Schlegel, J. Comput. Chem. 1982, 3, 214-218.
67. a) Farkas, PhD (CsC) Thesis, Eotvos Lorand University and Hungarian Academy of Sciences (Hungary), 1995
68. b) Farkas, H. B. Schlegel, Phys. Chem. Chem. Phys. 2002, 4, 11-15.