Insights on the mechanism of amine oxidation catalyzed by D-arginine dehydrogenase through pH and kinetic isotope effects

Journal of the American Chemical Society

Volumn 133, Issue 46, 2011, Pages 18957-18965

  Yuan, Hongling ^a   Xin, Yao ^a   Hamelberg, Donald ^a   Gadda, Giovanni ^a  

^a GEORGIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITE; AMINE OXIDATION; C-H BOND; COMPUTATIONAL STUDIES; DEUTERIUM KINETIC ISOTOPE EFFECT; ENZYME-SUBSTRATE COMPLEXES; FREE-ENERGY CALCULATIONS; HIGH RESOLUTION CRYSTAL STRUCTURE; KINETIC ISOTOPE EFFECTS; MECHANISTIC PROBES; MICHAELIS COMPLEX; MIXING TIME; OXIDATION REACTIONS; REDUCTION REACTION; SOLVENT VISCOSITY; STOPPED FLOW; SUBSTRATE BINDING; ZWITTERIONIC FORMS;

ARGININE; BINDING ENERGY; CARRIER MOBILITY; CATALYSIS; CRYSTAL STRUCTURE; DEUTERIUM; ENZYMES; FREE ENERGY; KINETICS; ORGANIC COMPOUNDS; OXIDATION; RATE CONSTANTS; REACTION KINETICS; SUBSTRATES;

PH EFFECTS;

DEXTRO ARGININE DEHYDROGENASE; OXIDOREDUCTASE; QUERCETIN; UNCLASSIFIED DRUG;

ARTICLE; CATALYSIS; CHEMICAL BOND; CHEMICAL REACTION; CHEMICAL REACTION KINETICS; ENERGY; ENZYME ACTIVE SITE; ENZYME ANALYSIS; ENZYME SUBSTRATE; ENZYME SUBSTRATE COMPLEX; ISOMERIZATION; OXIDATION; PH; SPECTROPHOTOMETER; VISCOSITY;

AMINES; ARGININE; CATALYSIS; CATALYTIC DOMAIN; D-AMINO-ACID OXIDASE; DEUTERIUM; FLAVINS; HYDROGEN-ION CONCENTRATION; KINETICS; MODELS, MOLECULAR; OXIDATION-REDUCTION; OXIDOREDUCTASES;

EID: 83055179279     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja2082729     Document Type: Article

References (60)

1. Edmondson, D. E.; Mattevi, A.; Binda, C.; Li, M.; Hubalek, F. Curr. Med. Chem. 2004, 11, 1983.
2. Thomas, T.; Thomas, T. J. Cell. Mol. Life Sci. 2001, 58, 244.
3. Pegg, A. E. Cancer Res. 1988, 48, 759.
4. Seiler, N.; Atanassov, C. L.; Raul, F. Int. J. Oncol. 1998, 13, 993.
5. Green, J.; Large, P. J. J. Gen. Microbiol. 1984, 130, 1947.
6. Wilce, M. C.; Dooley, D. M.; Freeman, H. C.; Guss, J. M.; Matsunami, H.; McIntire, W. S.; Ruggiero, C. E.; Tanizawa, K.; Yamaguchi, H. Biochemistry 1997, 36, 16116.
7. Mattevi, A.; Vanoni, M. A.; Todone, F.; Rizzi, M.; Teplyakov, A.; Coda, A.; Bolognesi, M.; Curti, B. Proc. Natl. Acad. Sci. U. S. A. 1996, 93, 7496.
8. Fitzpatrick, P. F. Arch. Biochem. Biophys. 2010, 493, 13.
9. Binda, C.; Newton-Vinson, P.; Hubalek, F.; Edmondson, D. E.; Mattevi, A. Nat. Struct. Biol. 2002, 9, 22.
10. De Colibus, L.; Li, M.; Binda, C.; Lustig, A.; Edmondson, D. E.; Mattevi, A. Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 12684.
11. Baker, P. J.; Waugh, M. L.; Wang, X. G.; Stillman, T. J.; Turnbull, A. P.; Engel, P. C.; Rice, D. W. Biochemistry 1997, 36, 16109.
12. Mure, M.; Mills, S. A.; Klinman, J. P. Biochemistry 2002, 41, 9269.
13. Kishishita, S.; Okajima, T.; Kim, M.; Yamaguchi, H.; Hirota, S.; Suzuki, S.; Kuroda, S.; Tanizawa, K.; Mure, M. J. Am. Chem. Soc. 2003, 125, 1041.
14. Umhau, S.; Pollegioni, L.; Molla, G.; Diederichs, K.; Welte, W.; Pilone, M. S.; Ghisla, S. Proc. Natl. Acad. Sci. U. S. A. 2000, 97, 12463.
15. Todone, F.; Vanoni, M. A.; Mozzarelli, A.; Bolognesi, M.; Coda, A.; Curti, B.; Mattevi, A. Biochemistry 1997, 36, 5853.
16. Denu, J. M.; Fitzpatrick, P. F. Biochemistry 1994, 33, 4001.
17. Kurtz, K. A.; Rishavy, M. A.; Cleland, W. W.; Fitzpatrick, P. F. J. Am. Chem. Soc. 2000, 122, 12896.
18. Ralph, E. C.; Anderson, M. A.; Cleland, W. W.; Fitzpatrick, P. F. Biochemistry 2006, 45, 15844.
19. Ralph, E. C.; Hirschi, J. S.; Anderson, M. A.; Cleland, W. W.; Singleton, D. A.; Fitzpatrick, P. F. Biochemistry 2007, 46, 7655.
20. Tilocca, A.; Gamba, A.; Vanoni, M. A.; Fois, E. Biochemistry 2002, 41, 14111.
21. McEwen, C. M., Jr.; Sasaki, G.; Jones, D. C. Biochemistry 1969, 8, 3952.
22. Paech, C.; Salach, J. I.; Singer, T. P. J. Biol. Chem. 1980, 255, 2700.
23. Silverman, R. B. Acc. Chem. Res. 1995, 28, 335.
24. Hanzlik, R. P.; Kishore, V.; Tullman, R. J. Med. Chem. 1979, 22, 759.
25. Edmondson, D. E.; Binda, C.; Mattevi, A. Arch. Biochem. Biophys. 2007, 464, 269.
26. Brown, L. E.; Hamilton, G. A. J. Am. Chem. Soc. 1970, 92, 7225.
27. Macmillar, S.; Edmondson, D. E.; Matsson, O. J. Am. Chem. Soc. 2011, 133, 12319.
28. Fu, G.; Yuan, H.; Li, C.; Lu, C. D.; Gadda, G.; Weber, I. T. Biochemistry 2010, 49, 8535.
29. Yuan, H.; Fu, G.; Brooks, P. T.; Weber, I. T.; Gadda, G. Biochemistry 2010, 49, 9542.
30. Li, C.; Yao, X.; Lu, C. D. Microbiology 2010, 156, 60.
31. Schowen, K. B.; Schowen, R. L. Methods Enzymol. 1982, 87, 551.
32. Lide, D. R. Handbook of Chemistry and Physics; CRC Press: Boca Raton, FL, 2000.
33. Weast, R. C.; Chemical Rubber Publishing Co. (CRC Press): Boca Raton, FL, 1981.
34. Warshel, A.; Sussman, F.; King, G. Biochemistry 1986, 25, 8368.
35. Simonson, T.; Carlsson, J.; Case, D. A. J. Am. Chem. Soc. 2004, 126, 4167.
36. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926.
37. Case, D. A.; Cheatham, T. E., 3rd; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M., Jr.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. J. Comput. Chem. 2005, 26, 1668.
38. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179.
39. Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Proteins 2006, 65, 712.
40. Xin, Y.; Hamelberg, D. RNA 2010, 16, 2455.
41. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577.
42. Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1997, 23, 327.
43. Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. J. Phys. Chem. 1993, 97, 10269.
44. Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. J. Comput. Chem. 2004, 25, 1157.
45. Karsten, W. E.; Lai, C.; Cook, P. F. J. Am. Chem. Soc. 1995, 117, 5914.
46. Venkatasubban, K. S.; Schowen, R. L. CRC Crit. Rev. Biochem. 1984, 17, 1.
47. Zhao, G.; Jorns, M. S. Biochemistry 2005, 44, 16866.
48. Cleland, W. W. I Enzyme Mechanism from Isotope Effects; CRC Press: Boca Raton, FL, 1991.
49. Edens, W. A.; Urbauer, J. L.; Cleland, W. W. Biochemistry 1997, 36, 1141.
50. Cleland, W. W. CRC Crit. Rev. Biochem. 1982, 13, 385.
51. In the crystal structure of DADH in complex with iminoargi-nine or iminohistidine, the flavin N (1) C (2) atoms are exposed to the bulk solvent and do not interact with the protein (see ref 30)., the flavin N (1) C (2) atoms are exposed to the bulk solvent and do not interact with the protein (see ref 30). This, along with the observation of an unprotonated hydroquinone at pH g7. 0, suggests that the pKa of the reduced flavin N (1) atom is minimally perturbed from the value of 6. 5 typically observed for reduced flavins in solution: Franken, H. D.; Rüterjans, H.; Müller, F. Eur. J. Biochem. 1984, 138, 481-9.
52. Ghisla, S.; Massey, V.; Lhoste, J. M.; Mayhew, S. G. Biochemistry 1974, 13, 589.
53. Zhao, G.; Jorns, M. S. Biochemistry 2002, 41, 9747.
54. Zhao, G.; Jorns, M. S. Biochemistry 2006, 45, 5985.
55. Edmondson, D. E.; Bhattacharrya, A. K.; Xu, J. Biochim. Biophys. Acta 2000, 1479, 52.
56. Sierks, M. R.; Sico, C.; Zaw, M. Biotechnol. Prog. 1997, 13, 601.
57. Ansari, A.; Jones, C. M.; Henry, E. R.; Hofrichter, J.; Eaton, W. A. Science 1992, 256, 1796.
58. Lindqvist, Y.; Bränden, C. I. J. Biol. Chem. 1989, 264, 3624.
59. Murray, M. S.; Holmes, R. P.; Lowther, W. T. Biochemistry 2008, 47, 2439.
60. Stenberg, K.; Clausen, T.; Lindqvist, Y.; Macheroux, P. Eur. J. Biochem. 1995, 228, 408.