Catalytic mechanism of the glycyl radical enzyme 4-hydroxyphenylacetate decarboxylase from continuum electrostatic and QC/MM calculations

Journal of the American Chemical Society

Volumn 135, Issue 39, 2013, Pages 14574-14585

  Feliks, Mikolaj ^a   Martins, Berta M ^b   Ullmann, G Matthias ^a  

^a UNIVERSITÄT BAYREUTH   (Germany)

^b HUMBOLDT UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CARBOXYLIC GROUP; CATALYTIC CYCLES; CATALYTIC FUNCTIONS; CATALYTIC MECHANISMS; FERMENTATIVE PRODUCTION; HYDROGEN-ATOM TRANSFER; PHENOLIC HYDROXYL GROUP; RADICAL ENZYMES;

ABSTRACTING; AMINO ACIDS; ATOMS; CARBON DIOXIDE; CARBOXYLATION; CATALYSIS; ELECTROSTATICS; ENZYMES; PROTON TRANSFER; SUBSTRATES; VOLATILE FATTY ACIDS;

FREE RADICAL REACTIONS;

CARBON DIOXIDE; CARBOXYLYASE; HYDROGEN; PHENOL; PROTON;

ARTICLE; DECARBOXYLATION; ELECTRON; POSITION; PROTON TRANSPORT; STATIC ELECTRICITY;

CARBOXY-LYASES; CATALYTIC DOMAIN; CLOSTRIDIUM; DECARBOXYLATION; MODELS, MOLECULAR; QUANTUM THEORY; STATIC ELECTRICITY;

EID: 84885092792     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja402379q     Document Type: Article

References (59)

1. Buckel, W.; Golding, B. FEMS Microbiol. Rev. 1998, 22, 523-541
2. Stubbe, J.; van der Donk, W. A. Chem. Rev. 1998, 98, 705-76
3. Eklund, H.; Fontecave, M. Struct. Fold. Des. 1999, 7, R257-R262
4. Frey, P. Annu. Rev. Biochem. 2001, 70, 121-148
5. Frey, P. A.; Hegeman, A. D.; Reed, G. H. Chem. Rev. 2006, 106, 3302-3316
6. Buckel, W.; Golding, B. T. Annu. Rev. Microbiol. 2006, 60, 27-49
7. Buckel, W. Angew. Chem., Int. Ed. 2009, 48, 6779-6787
8. Buckel, W.; Zhang, J.; Friedrich, P.; Parthasarathy, A.; Li, H.; Djurdjevic, I.; Dobbek, H.; Martins, B. M. Biochem. Biophys. Acta 2012, 1824, 1278-1290
9. Selmer, T.; Pierik, A.; Heider, J. Biol. Chem. 2005, 386, 981-988
10. Frey, P. A.; Hegeman, A. D.; Ruzicka, F. J. Crit. Rev. Biochem. Mol. Biol. 2008, 43, 63-88
11. Craciun, S.; Balskus, E. P. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 2130721312
12. Selmer, T.; Andrei, P. Eur. J. Biochem. 2001, 268, 1363-1372
13. Andrei, P.; Pierik, A.; Zauner, S.; Andrei-Selmer, L.; Selmer, T. Eur. J. Biochem. 2004, 271, 2225-2230
14. Yu, L.; Blaser, M.; Andrei, P. I.; Pierik, A. J.; Selmer, T. Biochemistry 2006, 45, 9584-9592
15. Dari, L.; Barker, H. Arch. Microbiol. 1985, 143, 311-312
16. Dawson, L. F.; Stabler, R. A.; Wren, B. W. J. Med. Microbiol. 2008, 57, 745-749
17. Martins, B. M.; Blaser, M.; Feliks, M.; Ullmann, G. M.; Buckel, W.; Selmer, T. J. Am. Chem. Soc. 2011, 133, 14666-14674
18. Vijh, A.; Conway, B. Chem. Rev. 1967, 67, 623-664
19. Himo, F.; Siegbahn, P. Chem. Rev. 2003, 103, 2421-2456
20. Lee, J.; Houk, K. Science 1997, 276, 942-945
21. Lee, T.; Chong, L.; Chodera, J.; Kollman, P. J. Am. Chem. Soc. 2001, 123, 12837-12848
22. Lundberg, M.; Blomberg, M.; Siegbahn, P. J. Mol. Model. 2002, 8, 119-130
23. Wang, J.; Dong, H.; Li, S.; He, H. J. Phys. Chem. B 2005, 109, 18664-18672
24. Silva, P.; Ramos, M. J. Phys. Chem. B 2005, 109, 18195-18200
25. Silva, P. J.; Ramos, M. J. J. Phys. Chem. B 2007, 111, 12883-12887
26. Moya-Garcia, A. A.; Ruiz-Pernia, J.; Marti, S.; Sanchez-Jimenez, F.; Tunon, I. J. Biol. Chem. 2008, 283, 12393-12401
27. Himo, F.; Eriksson, L. J. Am. Chem. Soc. 1998, 120, 11449-11455
28. Lucas, M.; Fernandes, P.; Eriksson, L.; Ramos, M. J. Phys. Chem. B 2003, 107, 5751-5757
29. Guo, J.; Himo, F. J. Phys. Chem. B 2004, 108, 15347-15354
30. Condic-Jurkic, K.; Perchyonok, V. T.; Zipse, H.; Smith, D. M. J. Comput. Chem. 2008, 29, 2425-2433
31. Condic-Jurkic, K.; Zipse, H.; Smith, D. M. J. Comput. Chem. 2010, 31, 1024-1035
32. Himo, F. J. Phys. Chem. B 2002, 106, 7688-7692
33. Himo, F. Biochim. Biophys. Acta 2005, 1707, 24-33
34. Himo, F. Chem. Phys. Lett. 2000, 328, 270-276
35. Hioe, J.; Savasci, G.; Brand, H.; Zipse, H. Chem.-Eur. J. 2011, 17, 3781-3789
36. Liu, Y.; Gallo, A. A.; Florian, J.; Liu, Y.-S.; Mora, S.; Xu, W. J. Phys. Chem. B 2010, 114, 5497-5502
37. Liu, Y.; Gallo, A. A.; Xu, W.; Bajpai, R.; Florian, J. J. Phys. Chem. A 2011, 115, 11162-11166
38. Feliks, M.; Ullmann, G. M. J. Phys. Chem. B 2012, 116, 7076-7087
39. Bashford, D.; Karplus, M. J. Phys. Chem. 1991, 95, 9556-9561
40. Ullmann, G. M.; Knapp, E. W. Eur. Biophys. J. 1999, 28, 533-551
41. Bombarda, E.; Ullmann, G. M. J. Phys. Chem. B 2010, 114, 1994-2003
42. Field, M. J. Comput. Chem. 2002, 23, 48-58
43. Senn, H. M.; Thiel, W. Angew. Chem.-Int. Edit. 2009, 48, 1198-1229
44. Galvan, I. F.; Field, M. J. J. Comput. Chem. 2008, 29, 139-143
45. Aleksandrov, A.; Field, M. Phys. Chem. Chem. Phys. 2012, 14, 12544-12553
46. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217
47. Brooks, B. R.; Brooks, C. L., III; Mackerell, A. D., Jr.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. J. Comput. Chem. 2009, 30, 1545-1614
48. MacKerell, A. D. J. Phys. Chem. B 1998, 102, 3586-3616
49. Torres, R.; Lovell, T.; Noodleman, L.; Case, D. J. Am. Chem. Soc. 2003, 125, 1923-1936
50. Bashford, D.; Gerwert, K. J. Mol. Biol. 1992, 224, 473-486
51. Ullmann, R. T.; Ullmann, G. M. J. Comput. Chem. 2012, 33, 887-900
52. Field, M. J. J. Chem. Theory Comput. 2008, 4, 1151-1161
53. Neese, F. Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2012, 2, 73-78
54. Vosko, S.; Wilk, L.; Nusair, M. Can. J. Phys. 1980, 58, 1200-1211
55. Lee, C.; Yang, W.; Parr, R. Phys. Rev. B 1988, 37, 785-789
56. Becke, A. J. Chem. Phys. 1993, 98, 5648-5652
57. Stephens, P.; Devlin, F.; Chabalowski, C.; Frisch, M. J. Phys. Chem. 1994, 98, 11623-11627
58. Flamholz, A.; Noor, E.; Bar-Even, A.; Milo, R. Nucleic Acids Res. 2012, 40, D770-D775
59. Humphrey, W.; Dalke, A.; Schulten, K. J. Mol. Graphics 1996, 14, 33-38