Anatomy of a simple acyl intermediate in enzyme catalysis: Combined biophysical and modeling studies on ornithine acetyle transterase

Journal of the American Chemical Society

Volumn 131, Issue 2, 2009, Pages 749-757

  Iqbal, Aman ^a   Clifton, Ian J ^a   Bagonis, Maria ^a   Kershaw, Nadia J ^a   Domene, Carmen ^a   Claridge, Timothy D W ^a   Wharton, Christopher W ^b   Schofield, Christopher J ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF BIRMINGHAM   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

[CARBONYL; ACETYL GROUPS; ACETYL TRANSFERASE; ACYL-ENZYME COMPLEX; AMINO GROUP; BACKBONE CARBONYL; BIOPHYSICAL ANALYSIS; CARBONYL OXYGEN; CRYSTALLINE STATE; CRYSTALLOGRAPHIC ANALYSIS; ENZYME CATALYSIS; ENZYME SUPERFAMILIES; HYDROLASE; HYDROLASES; IR ABSORPTION; IR ANALYSIS; IR SPECTROSCOPY; L-GLUTAMATE; MODELING APPROACH; MODELING STUDIES; N-TERMINAL; NMR ANALYSIS; NON-CATALYTIC; NUCLEOPHILIC CATALYSIS; OXYANION HOLE; SIDE-CHAIN; STRETCHING FREQUENCY; STRUCTURAL DATA;

ABSORPTION; AMIDES; AMINES; BINDING SITES; BIOPHYSICS; CARBONYLATION; CATALYSIS; COMPLEXATION; CRYSTAL STRUCTURE; CRYSTALLINE MATERIALS; HYDROGEN; HYDROGEN BONDS; INFRARED ABSORPTION; OXYGEN; POSITIVE IONS;

ENZYMES;

ACYLTRANSFERASE; HYDROGEN; HYDROLASE; ALPHA-CHYMOTRYPSIN; CHYMOTRYPSIN; CHYMOTRYPSIN A; GLUTAMATE ACETYLTRANSFERASE; GLUTAMIC ACID DERIVATIVE; N ACETYLGLUTAMIC ACID; N-ACETYLGLUTAMATE; PHENYLPROPIOLIC ACID; PHENYLPROPIONIC ACID DERIVATIVE;

ARTICLE; BIOPHYSICS; CRYSTALLOGRAPHY; ENZYME ACTIVE SITE; ENZYME ANALYSIS; ENZYME STRUCTURE; HYDROGEN BOND; INFRARED SPECTROPHOTOMETRY; MASS SPECTROMETRY; ACYLATION; CATALYSIS; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; METABOLISM; NUCLEAR MAGNETIC RESONANCE; X RAY CRYSTALLOGRAPHY;

ACETYLTRANSFERASES; ACYLATION; CATALYSIS; CHYMOTRYPSIN; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; GLUTAMATES; MODELS, CHEMICAL; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PHENYLPROPIONATES; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; SPECTROPHOTOMETRY, INFRARED;

EID: 62849090475     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja807215u     Document Type: Article

References (73)

1. Hedstrom, L. Chem. Rev. 2002, 102, 4501-4524.
2. Turk, B.; Turk, V.; Turk, D. Biol. Chem. 1997, 378, 141-150.
3. Artymiuk, P. J. NaJ. Struc Biol. 1995, 2, 1035-37.
4. Brannigan, J. A.; Dodson, G.; Duggleby, H. J.; Moody, P. C E.; Smith, J. L.; Tomchick, D. R.; Murzin, A. G. Nature 1995, 378, 416-419.
5. Matthews, B. W.; Sigler, P. B.; Henderson, R.; Blow, D. M. Nature 1967, 214, 652-656.
6. Wright, C S.; Alden, R. A.; Kraut, J. Nature 1969, 221, 235-42.
7. Freer, S. T.; Kraut. J.; Robertos, J. D.; Wright, H. T.; Xuong, N. H. Biochemistry 1970, 9, 1997-2009.
8. Henderson, R. J. Mol. Biol. 1970, 54, 341-54.
9. Hedstrom, L. Curr. Protoc. Prot. Sci. 2002, 21, 21-10.
10. Dodson, G.; Wlodawer, A. Trends Biochem. Sci. 1998, 23, 347-352.
11. Oinonen, C; Rouvinen, J. Protein Sci. 2000, 9, 2329-2327.
12. Wang, Z.; Fast, W.; Valentine, A. M.; Benkovic, S. J. Curr. Op. Chem. Biol. 1999, 3, 614-622.
13. Philippon, A.; Dusart, J.; Joris, B.; Frère, J. M. Cell. Mol. Life Sci. 1998, 54, 341-346.
14. Page, M.; Di Cera, E. Cell. Mol. Life Sci. 2008, 65, 1220-1236.
15. Lowther, W. T.; Matthews, B. W. Chem. Rev. 2002, 102, 4581-4608.
16. Powers, J. C,; Asgian, J. L.; Ekici, O. D.; James, K. E. Chem. Rev. 2002, 102, 4639-4750.
17. Leung-Toung, R.; Zhao, Y.; Li, W.; Tarn, T. F.; Karimian, K.; Spino, M. Curr. Med. Chem. 2006, 13, 547-581.
18. Kisselev, A. F.; Goldberg, A. L. Chem. Biol. 2001, 8, 739-758.
19. Malcolm, G.; Page, P. Drus Resist. Updates 2000, 3, 109-125.
20. Ding, X.; Rasmussen, B. F.; Petsko, G. A.; Ringe, D. Bjochemistiy 1994, 33, 9285-9293.
21. Dixon, M. M.; Brennan, R. G.; Matthews, B. W. Int. J. Biol. Macromol. 1991, 13, 89-96.
22. Blanchard, H.; James, M. N. G. J. Mol. Biol. 1994, 241, 574-587.
23. Ding, X.; Rasmussen, B. F.; Petsko, G. A.; Ringe. D. Bioorg. Chem. 2006, 34, 410-423.
24. Liu, B.; Schofield, C J.; Wilmouth, R. C. J. Biol. Chem. 2006, 281, 24024-24035.
25. Wilmouth, R. C; Clifton, I. J.; Robinson, C V.; Roach, P. L.; Aplin, R. T.; Westwood, N. J.; Hajdu. J.; Schofield, C. J. Nat. Struct. Biol. 1997, 4, 456-462.
26. Wilmouth, R. C; Edman, K.; Neutze, R.; Wright, P. A.; Clifton, I. J.; Schneider, T. R.; Schofield, C J.; Hajdu, J. Nat. Struct. Biol. 2001, 8, 689-694.
27. Katona, G.; Wilmouth, R. C; Wright, P. A.; Berglund, G. I; Hajdu, J.; Neutze, R.; Schofield, C. J. J.Biol. Chem. 2002, 277, 21962-21970.
28. Radisky, E. S.; Lee, J. M.; Lu. C. J.; Koshland, D. E. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 6835-6840.
29. Vivares, D.; Arnoux, P.; Pignol, D. Prpc. Natl. Acad. Sci. U.S.A. 2005, 102, 18848-18853.
30. Lee, J.; Feldman, A. R.; Delmas, B.; Paetzel, M. J. Biol. Chem. 2007, 282, 24928-24937.
31. Wilmouth, R. C; Clifton, I. J.; Neutze, R. Nat. Prod. Rep. 2000, 17, a 527-533.
32. Wilkinson, A. S.; Bryant, P. K.; Meroueh, S. O.; Page, M. G.; Mobashery,. S.; Wharton, C. W. Biochemistry 2003, 42, 1950-1957.
33. Wilkinson, A. S.; Ward, S.; Kania, M.; Page. M. G.; Wharton. C. W. Biochemistry 1999, 38, 3851-3856.
34. Johal, S. S.; White, A. J.; Wharton, C. W. Biochem. J. 1994, 297, 281-287.
35. Nukaga, M.; Bethel, C. R.; Thomson, J. M.; Hujer, A. M.; Distler, A.; Anderson, V. E.; Knox. J. R.; Bonomo, R. A. J. Am. Chem. Soc. 2008,
36. Mavevraud, L.; Mourey, L.; Kotra, L. P.; Pedelacq, J. D.; Guillet, V.; Mobashery, S.; Samama, J. P.J. am. Chem. Soc. 1998, 120, 97489752.
37. Beadle, B. M.; Shoichet, B. K. Antimictob. Agents Chemother. 2002, 46, 3978-3980.
38. McVey, C. E.; Walsh, M. A.; Dodson, G. G.; Wilson, K. S.; Brannigan, J. A. J. Mol. Biol. 2001, 313, 139-150.
39. Michalska, K.; Bujacz, G.; Jaskolski, M. J. Mol. Biol. 2006, 360, 10516.
40. Smith JL. Z. E.; Wery, J. P.; Niu, L.; Switzer. R. L.; Zalkin, H.; Satow. Y. Nature 1994, 264, 1427-33.
41. Okada, T.; Suzuki, H.; Wada, K.; Kumagai, H.; Fukuvama, K. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 6471-6476.
42. Groll. M.; Huber, R. Biochim. Biophys. Acta 2004, 29, 33-44.
43. Seemuller. E.; Lupas, A.; Baumeister, W. Nature 1996, 382, 468471.
44. Marc, F.; Weigel, P.; Legrain, C.; Aimeras. Y.; Santrot, M.; Glansdorff, N.; Sakanyan, Y. Eur. J. Biochem. 2000, 267, 5217-5226.
45. Kershaw, N. J.; McNaughton, H. J.; Hewitson, K. S.; Hernandez, H.; Griffin, J.; Hughes, C.; Greaves, P.; Barton, B.; Robinson, C V.; Schofield, C. J. Eur. J. Biochem. 2002, 269, 2052-2059.
46. Sleeman, M. C; Sorensen, J. L.; Batchelar, E. T.; McDonough, M. A.; Schofield, C. J. J. Biol. Chem. 2005, 280, 34956-34965.
47. Otwinowski, Z.; Minor, W. Methods Enzvmol. 1997, 276, 307-326.
48. CCP4 project. Acta. Crystallogr. D1994, D50, 760-763.
49. Read, R. J. Acta. Crystallogr. D 2001, D57, 1373-1382.
50. Murshudov, G. N.; Vagin, A. A.; Dodson, E. J. Acta Crystallogr. D 1997, D53, 250-255.
51. Jones. T. A.; Zou. J.-Y.; Cowan, S. W.; Kjeldgaard, M. Acta Crystallogr. A 1991, A47, 110-119.
52. Emsley, P.; Cowtan. K. Acta Crystallogr. D 2004, D60, 2126-2132.
53. Hooft. R. W. W.; Vriend. G.; Sander, C; Abola, E. E. Nature 1996, 381, 272.
54. Laskowski. R. A.; MacArthur, M. W.; Moss, D. S.; Thornton, J. M. J. Appl. Crystallogr. 1993, 26, 283-291.
55. Painter, J.; Merritt. E. A. J. Appl. Cnystallogr. 2006, 39, 109-111.
56. Laxmikant, K.; Robert, S.; Milind, B.; Robert, B.; Attila, G.; Neal, K.; James. P.; Artiomo, S.; Krishnan, V.; Klaus, S. J. Comput. Phys. 1999, 151, 283-312.
57. Neria. E.; Fischer. S., a.; Karplus, M. J. Chem. Phys. 1996, 105, 19021921.
58. Fang. B.; Martyna, G.; Deng, Y. Comput. Phys. Commun. 2007, 177, 362-377.
59. Berendsen, H. J. C; Postma. J. P. M.; Van Gunsteren, W. F.; Dinola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684-3690.
60. Martyna, G. J.; Tobias, D. J.; Klein, M. L. J. Chem. Phys. 1994, 101, 4177-4189.
61. Niu, C. H.; Shindo, H.; Cohen, J. S.; Cross, M. J. Am. Chem. Soc. 1977, 99, 3161-3162.
62. Chaloner, P. A. J. Perkin Trans. 1980, 2, 1028-1035.
63. Yoshida. N.; Yamasaki, M.; Ishii. S.-I. J. Biochem. 1973,1973, 11751183.
64. Elkins, J. M.; Kershaw. N. J.; Schofield. C. J. Biochem. J. 2005, 385, 565-573.
65. Vaguine, A. A.; Richelle. J.; Wodak, S. J. Acta Crystallogr. D 1999, 55, 191-205.
66. Brünger, A. T.; Adams, P. D.; Clore, G. M.; DeLano, W. L.; Gros, P.; Grosse-Kunstleve, R. W.; Jiang, J.-S.; Kuszewski, J.; Nilges, M.; Pannu, N. S.; Read, R. J.; Rice, L. M.; Simonson, T.; Warren, G. L. Acta Crystallogr. D 1998, 54, 905-921.
67. Deslongchamps, P. Stereoelectronic Effects in Organic Chemistry; Pergamon Press: New York, 1983; Chapter 3.
68. White, A. J.; Drabble, K.; Ward, S.; Wharton, C. W. Biochem. J. 1992, 2S7, 317-323.
69. Mendes, P. Trends Biochem. Sci. 1997, 22, 361-363.
70. Barth, A.; Zscherp, C. Q. Rev. Biophys. 2002, 35, 369-130.
71. Mackenzie, N. E.; Malthouse. J. P.; Scott, A. I. Biochem. J. 1984, 219, 437-444.
72. Li, J. J.; Li, C; Blindauer, C. A.; Bugg, T. D. Bjochemistiy 2006, 45, 12461-12469.
73. Szeltner, Z.; Renner, V.; Polgár, L. Protein Sci. , 9, 353-360.