Mechanism for catechol ring cleavage by non-heme iron intradiol dioxygenases: A hybrid DFT study

Journal of the American Chemical Society

Volumn 128, Issue 39, 2006, Pages 12941-12953

  Borowski, Tomasz ^a   Siegbahn, Per E M ^b  

^a INSTITUTE OF CATALYSIS AND SURFACE CHEMISTRY   (Poland)

^b STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

CATECHOL RING CLEAVAGE; CONFORMATIONAL CHANGE; FIRST SHELL LIGANDS; NON HEME IRON INTRADIOL DIOXYGENASES;

CATALYSIS; DISCRETE FOURIER TRANSFORMS; MOLECULAR STRUCTURE; PROBABILITY DENSITY FUNCTION; REACTION KINETICS; SUBSTRATES;

PROTEINS;

ACID ANHYDRIDE; ACYCLIC HYDROCARBON SUBSTITUENT; ARGININE; CARBON; CATECHOL; DIOXYGENASE; GLUTAMINE; HISTIDINE; HYDROPEROXIDE DERIVATIVE; IRON; LIGAND; METAL; OXYGEN; PEROXIDE; PROTOCATECHUATE 3,4 DIOXYGENASE; TYROSINE; WATER;

ARTICLE; ATOM; CHEMICAL REACTION; CONFORMATIONAL TRANSITION; COVALENT BOND; DENSITY FUNCTIONAL THEORY; ELECTRON TRANSPORT; ENZYME ACTIVITY; ENZYME BINDING; ENZYME MECHANISM; ENZYME SUBSTRATE; HYDROLYSIS; LIGAND BINDING; MATHEMATICAL ANALYSIS; METAL BINDING; MOLECULAR MODEL; OXYGEN AFFINITY; PEROXIDATION; PROTON TRANSPORT; REACTION ANALYSIS; RING OPENING;

ANHYDRIDES; CATECHOLS; CRYSTALLOGRAPHY, X-RAY; HYDROLYSIS; MODELS, MOLECULAR; NONHEME IRON PROTEINS; OXYGEN; PROTEIN CONFORMATION; PROTOCATECHUATE-3,4-DIOXYGENASE; THERMODYNAMICS;

EID: 33749534288     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja0641251     Document Type: Article

References (40)

1. Fujisawa, H.; Hayaishi, O. J. Biol. Chem. 1968, 243, 2673-2681.
2. Brown, C. K.; Vetting, M. W.; Earhart, C. A.; Ohlendorf, D. H. Annu. Rev. Microbiol. 2004, 58, 555-585.
3. Costas, M.; Mehn, M. P.; Jensen, M. P.; Que, L. Chem. Rev. 2004, 104, 939-986.
4. Que, L., Jr.; Ho, R. Y. N. Chem. Rev. 1996, 96, 2607-2624.
5. Ryle, M. J.; Hausinger, R. P. Curr. Opin. Chem. Biol. 2002, 6, 193-201.
6. Bugg, T. D. H. Tetrahedron 2003, 59, 7075-7101.
7. Bugg, T. D. H. Curr. Opin. Chem. Biol. 2001, 5, 550-555.
8. Bugg, T. D. H.; Winfield, C. J. Nat. Prod. Rep. 1998, 513-530.
9. Solomon, E. S.; Brunold, T. C.; Davis, M. I.; Kemsley, J. N.; Lee, S. K.; Lehnert, N.; Neese, F.; Skulan, A. J.; Yang, Y. S.; Zhou, J. Chem. Rev. 2000, 100, 235-349.
10. Ohlendorf, D.; Orville, A.; Lipscomb. J. J. Mol. Biol. 1994, 244, 586-608.
11. Davis, M. I.; Orville, A. M.; Neese, F.; Zaleski, J. M.; Lipscomb, J. D.; Solomon, E. I. J. Am. Chem. Soc. 2002, 124, 602-614.
12. Siu, D.; Orville, A.; Lipscomb, J.; Ohlendorf, D.; Que, L. Biochemistry 1992, 31, 10443-10448.
13. Orville, A.; Lipscomb, J. J. Biol. Chem. 1989, 264, 8791-8801.
14. Whittaker, J.; Lipscomb, J. J. Biol. Chem. 1984, 259, 4487-4495.
15. Horsman, G. P.; Jirasek, A.; Vaillancourt, F. H.; Barbosa, C. J.; Jarzecki, A. A.; Xu, C.; Mekmouche, Y.; Spiro, T. G.; Lipscomb, J. D.; Blades, M. W.; Turner, R. F. B.; Eltis, L. D. J. Am. Chem. Soc. 2005, 127, 16882-16891.
16. Tyson, C. A. J. Biol. Chem. 1975, 250, 1765-1770.
17. Orville, A.; Elango, N.; Lipscomb, J.; Ohlendorf, D. Biochemistry 1997, 36, 10039-10051.
18. Orville, A.; Lipscomb, J.; Ohlendorf, D. Biochemistry 1997, 36, 10052-10066.
19. Valley, M. P.; Brown, C. K.; Burk, D. L.; Vetting, M. W.; Ohlendorf, D. H.; Lipscomb, J. D. Biochemistry 2005, 44, 11024-11039.
20. Funabiki, T.; Yamazaki, T. J. Mol. Cal. A 1999, 150, 37-47.
21. Bull, C.; Ballou, D.; Otsuka, S. J. Biol. Chem. 1981, 256, 12681-12686.
22. Frazee, R.; Orville, A.; Dolbeare, K.; Yu, H.; Ohlendorf, D.; Lipscomb, J. Biochemistry; 1998, 37, 2131-2144.
23. Dorn, E.; Knackmuss, H.-J. Biochem. J. 1978, 174, 85-94.
24. Walsh, T. A.; Ballou, D. P.; Mayer, R.; Que, L.. Jr. J. Biol. Chem. 1983, 258, 14422-14427.
25. Walsh, T. A.; Ballou, D. J. Biol. Chem. 1983. 258, 14413-14421.
26. Fujiwara, M.; Golovleva, L.; Saeki, Y.; Nozaki, M.; Hayaishi, O. J. Biol. Chem. 1975, 250, 4848-4855.
27. Becke, A. D. J. Chem. Phys. 1993, 98, 5648-5652.
28. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. 1988, B37, 785-789.
29. Frisch, M. J. et al. Gaussian 03. revision B. 03; Gaussian Inc.: Pittsburgh, PA, 2003.
30. JAGUAR 5.5; Schrödinger. Inc.: Portland, OR, 2005.
31. Tannor, D. J.; Marten, B.; Murphy, R.; Friesner, R. A.; Sitkoff, D.; Nicholls, A.; Ringnalda, M.; Goddard, W. A., III; Honig, B. J. Am. Chem. Soc. 1994, 116, 11875-11882.
32. Marten, B.; Kim, K.; Cortis, C.; Friesner, R. A.; Murphy, R.; Ringnalda, M.; Sitkoff, D.; Honig, B. J. Phys. Chem. 1996, 100, 11775-11788.
33. Montgomery, J., Jr.; Frisch, M.; Ochterski, J.; Petersson, G. J. Chem. Phys. 1999, 110, 2822-2827.
34. Humphrey, W.; Dalke, A.; Schulten, K. J. Mol. Graph. 1996, 14, 33-38.
35. Persistence of Vision Raytracer, version 3.6; Persistence of Vision Pty. Ltd.: Williamstown, Victoria, Australia. 2004; retrieved from http://www.povray.org/download/.
36. Portmann, S.; Lüthi, H. P. CHIMIA 2000, 54, 766-770.
37. Siegbahn, P. E. M.; Haeffner, F. J. Am. Chem. Soc. 2004, 126, 8919-8932.
38. Borowski, T.; Georgiev, V.; Siegbahn, P. E. M. J. Am. Chem. Soc. 2005, 127, 17303-17314.
39. Georgiev, V.; Borowski, T.; Siegbahn, P. E. M. J. Biol. Inorg. Chem. 2006, 11, 571-585.
40. Sawaki, Y.; Ogata, Y. J. Am. Chem. Soc. 1975, 97, 6983-6989.