Expanding the Catalytic Triad in Epoxide Hydrolases and Related Enzymes

ACS Catalysis

Volumn 5, Issue 10, 2015, Pages 5702-5713

  Amrein, Beat A ^a   Bauer, Paul ^a   Duarte, Fernanda ^a   Janfalk Carlsson, Åsa ^b   Naworyta, Agata ^a   Mowbray, Sherry L ^a   Widersten, Mikael ^b   Kamerlin, Shina C L ^a  

^a SCIENCE FOR LIFE LABORATORY   (Sweden)

^b UPPSALA UNIVERSITY   (Sweden)

Author keywords

biocatalysis; empirical valence bond; enzyme selectivity; potato epoxide hydrolase; StEH1; trans stilbene oxide; X ray crystallography

Indexed keywords

BIOCATALYSTS; CATALYSIS; CELL IMMOBILIZATION; CRYSTALLOGRAPHY; HYDROLASES; REGIOSELECTIVITY; STEREOCHEMISTRY; SUBSTRATES; X RAY CRYSTALLOGRAPHY;

BIOCATALYSIS; EPOXIDE HYDROLASES; STEH1; TRANS-STILBENE OXIDES; VALENCE BONDS;

ENZYMES;

EID: 84943146343     PISSN: 21555435     EISSN: None     Source Type: Journal    
DOI: 10.1021/acscatal.5b01639     Document Type: Article

References (57)

1. Morisseau, C.; Hammock, B. D. Annu. Rev. Pharmacol. Toxicol. 2005, 45, 311-333 10.1146/annurev.pharmtox.45.120403.095920
2. Archelas, A.; Furstoss, R. Curr. Opin. Chem. Biol. 2001, 5, 112-119 10.1016/S1367-5931(00)00179-4
3. Monterde, M. I.; Lombard, H.; Archelas, A.; Cronin, A.; Arand, A.; Furstoss, R. Tetrahedron: Asymmetry 2004, 15, 2801-2805 10.1016/j.tetasy.2004.06.032
4. Elfström, L. T.; Widersten, M. Biochem. J. 2005, 390, 633-640 10.1042/BJ20050526
5. Elfström, L. T.; Widersten, M. Biochemistry 2006, 45, 205-212 10.1021/bi051893g
6. Thomaeus, A.; Carlsson, J.; Åqvist, J.; Widersten, M. Biochemistry 2007, 46, 2466-2479 10.1021/bi062052s
7. Thomaeus, A.; Naworyta, A.; Mowbray, S. L.; Widersten, M. Protein Sci. 2008, 17, 1275-1284 10.1110/ps.034173.107
8. Lindberg, D.; de la Fuente Revenga, M.; Widersten, M. Biochemistry 2010, 49, 2297-2304 10.1021/bi902157b
9. Carlsson, Å. J.; Bauer, P.; Ma, H.; Widersten, M. Biochemistry 2012, 51, 7627-7637 10.1021/bi3007725
10. Wu, S.; Chen, Y.; Xu, Y.; Li, A.; Xu, Q.; Glieder, A.; Li, Z. ACS Catal. 2014, 4, 409-420 10.1021/cs400992z
11. Hopmann, K. H.; Himo, F. Chem.-Eur. J. 2006, 6, 6898-6909 10.1002/chem.200501519
12. Lonsdale, R.; Hoyle, S.; Grey, D. T.; Ridder, L.; Mulholland, A. J. Biochemistry 2012, 51, 1774-1786 10.1021/bi201722j
13. Warshel, A.; Weiss, R. M. J. Am. Chem. Soc. 1980, 102, 6218-6226 10.1021/ja00540a008
14. Warshel, A. Computer Modeling of Chemical Reactions in Enzymes and Solutions, 1 st ed.; Wiley: New York, 1991.
15. Frushicheva, M. P.; Warshel, A. ChemBioChem 2012, 13, 215-223 10.1002/cbic.201100600
16. Schopf, P.; Warshel, A. Proteins: Struct., Funct., Genet. 2014, 82, 1387-1399 10.1002/prot.24506
17. Lind, M. E. S.; Himo, F. Angew. Chem., Int. Ed. 2013, 52, 4563-4567 10.1002/anie.201300594
18. Mowbray, S. L.; Elfström, T. L.; Ahlgren, K. M.; Andersson, C. E.; Widersten, M. Protein Sci. 2006, 15, 1628-1637 10.1110/ps.051792106
19. Reetz, M. T.; Bocola, M.; Wang, L.-W.; Sanchis, J.; Cronin, A.; Arand, M.; Zou, J.; Archelas, A.; Bottalla, A.-L.; Naworyta, A.; Mowbray, S. L. J. Am. Chem. Soc. 2009, 131, 7334-7343 10.1021/ja809673d
20. Hopmann, K. H.; Himo, F. J. Phys. Chem. B 2006, 110, 21299-21310 10.1021/jp063830t
21. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. Nucleic Acids Res. 2000, 28, 235-242 10.1093/nar/28.1.235
22. Chen, V. B.; Arendall, W. B.; Headd, J. J.; Keedy, D. A.; Immormino, R. M.; Kapral, G. J.; Murray, L. W.; Richardson, J. S.; Richardson, D. C. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2010, 66, 12-21 10.1107/S0907444909042073
23. Olsson, M. H. M.; Søndergaard, C. R.; Rostkowski, M.; Jensen, J. H. J. Chem. Theory Comput. 2011, 7, 525-537 10.1021/ct100578z
24. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J. J. Am. Chem. Soc. 1996, 118, 11225-11236 10.1021/ja9621760
25. Marelius, J.; Kolmodin, K.; Feierberg, I.; Åqvist, J. J. Mol. Graphics Modell. 1998, 16, 213-225 10.1016/S1093-3263(98)80006-5
26. Schrödinger, release 2013-3: MacroModel, version 9.1, Schrödinger, LLC: New York, 2013.
27. Cieplak, P.; Cornell, W. D.; Bayly, C.; Kollman, P. A. J. Comput. Chem. 1995, 16, 1357-1377 10.1002/jcc.540161106
28. King, G.; Warshel, A. J. Chem. Phys. 1989, 91, 3647-3661 10.1063/1.456845
29. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935 10.1063/1.445869
30. Aqvist, J.; Kamerlin, S. C. L. Biochemistry 2015, 54, 546-556 10.1021/bi501373g
31. Lee, F. S.; Warshel, A. J. Chem. Phys. 1992, 97, 3100-3107 10.1063/1.462997
32. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327-341 10.1016/0021-9991(77)90098-5
33. Berendsen, H. J. C.; Postma, J. P. M.; Vangunsteren, W. F.; Dinola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-3690 10.1063/1.448118
34. Kamerlin, S. C. L.; Warshel, A. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2011, 1, 30-45 10.1002/wcms.10
35. Roca, M.; Vardi-Kilshtain, A.; Warshel, A. Biochemistry 2009, 48, 3046-3056 10.1021/bi802191b
36. Frushicheva, M. P.; Cao, J.; Chu, Z. T.; Warshel, A. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 16869-16874 10.1073/pnas.1010381107
37. Frushicheva, M. P.; Cao, J.; Warshel, A. Biochemistry 2011, 50, 3849-3858 10.1021/bi200063a
38. Warshel, A.; Sharma, P. K.; Kato, M.; Xiang, Y.; Liu, H. B.; Olsson, M. H. M. Chem. Rev. 2006, 106, 3210-3235 10.1021/cr0503106
39. Warshel, A. Annu. Rev. Biophys. Biomol. Struct. 2003, 32, 425-443 10.1146/annurev.biophys.32.110601.141807
40. Wolfenden, R.; Snider, M. Acc. Chem. Res. 2001, 34, 938-945 10.1021/ar000058i
41. McClelland, R. A.; Kanagasabapathy, V. M.; Steenken, S. Can. J. Chem. 1990, 68, 375-382 10.1139/v90-057
42. Hwang, J. K.; King, G.; Creighton, S.; Warshel, A. J. Am. Chem. Soc. 1988, 110, 5297-5311 10.1021/ja00224a011
43. Davies, M. N.; Toseland, C. P.; Moss, D. S.; Flower, D. R. BMC Biochem. 2006, 7, 18 10.1186/1471-2091-7-18
44. Lenfant, N.; Hotelier, T.; Velluet, E.; Bourne, Y.; Marchot, P.; Chatonnet, A. Nucleic Acids Res. 2013, 41, D423-D429 10.1093/nar/gks1154
45. Sievers, F.; Wilm, A.; Dineen, D.; Gibson, T. J.; Karplus, K.; Li, W. Z.; Lopez, R.; McWilliam, H.; Remmert, M.; Soding, J.; Thompson, J. D.; Higgins, D. G. Mol. Syst. Biol. 2011, 7, 539 10.1038/msb.2011.75
46. Crooks, G. E.; Hon, G.; Chandonia, J. M.; Brenner, S. E. Genome Res. 2004, 14, 1188-1190 10.1101/gr.849004
47. Altschul, S. F.; Gish, W.; Miller, W.; Myers, E. W.; Lipman, D. J. J. Mol. Biol. 1990, 215, 403-410 10.1016/S0022-2836(05)80360-2
48. Winn, M. D.; Ballard, C. C.; Cowtan, K. D.; Dodson, E. J.; Emsley, P.; Evans, P. R.; Keegan, R. M.; Krissinel, E. B.; Leslie, A. G. W.; McCoy, A.; McNicholas, S. J.; Murshudov, G. N.; Pannu, N. S.; Potterton, E. A.; Powell, H. R.; Read, R. J.; Vagin, A.; Wilson, K. S. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2011, 67, 235-242 10.1107/S0907444910045749
49. Leslie, A. G. W.; Powell, H. R. In Evolving Methods for Macromolecular Crystallography; Read, R. J.; Sussman, J. L., Eds.; NATO Science Series II, Vol. 245; Springer: Dordrecht, The Netherlands, 2007; pp 41-51.
50. Evans, P. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2006, 62, 72-82 10.1107/S0907444905036693
51. Murshudov, G. N.; Skubak, P.; Lebedev, A. A.; Pannu, N. S.; Steiner, R. A.; Nicholls, R. A.; Winn, M. D.; Long, F.; Vagin, A. A. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2011, 67, 355-367 10.1107/S0907444911001314
52. Jones, T. A.; Zou, J. Y.; Cowan, S. W.; Kjeldgaard, M. Acta Crystallogr., Sect. A: Found. Crystallogr. 1991, 47, 110-119 10.1107/S0108767390010224
53. Emsley, P.; Lohkamp, B.; Scott, W. G.; Cowtan, K. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2010, 66, 486-501 10.1107/S0907444910007493
54. Rink, R.; Fennema, M.; Smids, M.; Dehmel, U.; Janssen, D. B. J. Biol. Chem. 1997, 272, 14650-14657 10.1074/jbc.272.23.14650
55. Muegge, I.; Tao, H.; Warshel, A. Protein Eng., Des. Sel. 1997, 10, 1363-1372 10.1093/protein/10.12.1363
56. Robillard, G.; Shulman, R. G. J. Mol. Biol. 1972, 71, 507-511 10.1016/0022-2836(72)90366-X
57. Wijma, H. J.; Floor, R. J.; Bjelic, S.; Marrink, S. J.; Baker, D.; Janssen, D. B. Angew. Chem., Int. Ed. 2015, 54, 3726-3730 10.1002/anie.201411415