DFT investigation on the mechanism of the deacetylation reaction catalyzed by LpxC

Journal of Physical Chemistry B

Volumn 112, Issue 11, 2008, Pages 3462-3469

  Robinet, Jesse J ^a   Gauld, James W ^a  

^a UNIVERSITY OF WINDSOR   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ACETYLATION; BACTERIA; CELL MEMBRANES; DENSITY FUNCTIONAL THEORY; DISCRETE FOURIER TRANSFORMS; FOOD ADDITIVES; LIPIDS; MECHANISMS; PROBABILITY DENSITY FUNCTION; ZINC;

ACTIVE SITES; BIOCHEMICAL SYNTHESIS; DEACETYLATION (DD); LIPID A; PATHOGENIC BACTERIA; REACTION CATALYZED;

BINDING SITES;

AMIDASE; CARBON; GLUTAMIC ACID; HISTIDINE; LPXC DEACETYLASE, PSEUDOMONAS; NITROGEN; OXYGEN; PROTON; THREONINE; WATER; ZINC;

ARTICLE; BINDING SITE; BIOLOGY; CATALYSIS; CHEMICAL MODEL; CHEMISTRY; ENZYME SPECIFICITY; HYDROGEN BOND; HYDROXYLATION; METABOLISM; METHODOLOGY; THERMODYNAMICS;

AMIDOHYDROLASES; BINDING SITES; CARBON; CATALYSIS; COMPUTATIONAL BIOLOGY; GLUTAMIC ACID; HISTIDINE; HYDROGEN BONDING; HYDROXYLATION; MODELS, CHEMICAL; NITROGEN; OXYGEN; PROTONS; SUBSTRATE SPECIFICITY; THERMODYNAMICS; THREONINE; WATER; ZINC;

EID: 45949084971     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp075415m     Document Type: Article

References (45)

1. Onishi, H. R.; Pelak, B. A.; Gerckens, L. S.; Silver, L. L.; Kahan, F. M.; Chen, M.-H.; Patchett, A. A.; Galloway, S. M.; Hyland, S. A.; Anderson, M. S.; Raetz, C. R. H. Science 1996, 274, 980.
2. Jackman, J. E.; Fierke, C. A.; Tumeyi, L. N.; Pirrungi, M.; Uchiyama, T.; Tahir, S. H.; Hindsgaul, O.; Raetz, C. R. H. J. Biol. Chem. 2000, 275, 11002.
3. Clements, J. M.; Coignard, F.; Johnson, I.; Chandler, S.; Palan, S.; Waller, A.; Wijkmans, J.; Hunter, M. G. Antimicrob. Agents Chemother. 2002, 46, 1793.
4. White, R. J.; Margolis, P. S.; Trias, J.; Yuan, Z. Curr. Opin. Pharmacol. 2003, 3, 502.
5. McClerren, A. L.; Endsley, S.; Bowman, J. L.; Andersen, N. H.; Guan, Z.; Rudolph, J.; Raetz, C. R. H. Biochemistry 2005, 44, 16574.
6. Mdluli, K. E.; Witte, P. R.; Kline, T.; Barb, A. W.; Erwin, A. L.; Mansfield, B. E.; McClerren, A. L.; Pirrung, M. C.; Tumey, L. N.; Warrener, P.; Raetz, C. R. H.; Stover, C. K. Antimicrob. Agents Chemother. 2006, 50, 2178.
7. Barb, A. W.; McClerren, A. L.; Snehelatha, K.; Reynolds, C. M.; Zhou, P.; Raetz, C. R. H. Biochemistry 2007, 46, 3793.
8. Kadam, R. U.; Chavan, A.; Roy, N. Bioorg. Med. Chem. Lett. 2007, 17, 861.
9. Andersen, M. S.; Bull, H. G.; Galloway, S. M.; Kelly, T. M.; Mohan, S.; Radika, K.; Raetz, C. R. H. J. Biol. Chem. 1993, 265, 19858.
10. Raetz, C. R. H.; Whitfield, C. Annu. Rev. Biochem. 2002, 71, 635.
11. Jackman, J. E.; Raetz, C. R. H.; Fierke, C. A. Biochemistry 1999, 35, 1902.
12. Jackman, J. E.; Raetz, C. R. H.; Fierke, C. A. Biochemistry 2001, 40, 514.
13. McClure, C. P.; Rusche, K. M.; Peariso, K.; Jackman, J. E.; Fierke, C. A.; Penner-Hahn, J. E. J. Inorg. Biochem. 2003, 94, 78.
14. Whittington, D. A.; Rusche, K. M.; Shin, H.; Fierke, C. A.; Christianson, D. W. Proc. Nat. Acad, Sci. U.S.A. 2003, 100, 8146.
15. Vallee, B. L.; Auld, D. S. Biochemistry 1990, 29, 5647.
16. Hernick, M.; Fierke, C. A. Arch. Biochem. Biophys. 2005, 433, 71.
17. Gennadios, H. A.; Whittington, D. A.; Li, X.; Fierke, C. A.; Christianson, D. W. Biochemistry 2006, 45, 7940.
18. Lipscomb, W. N.; Sträter, N. Chem. Rev. 1996, 96, 2375.
19. Coggins, B. E.; Li, X.; McClerren, A. L.; Hindsgaul, O.; Raetz, C. R. H.; Zhou, P. Nat. Struct. Biol. 2003, 10, 645.
20. Coggins, B. E.; McClerren, A. L.; Jiang, L.; Li, H.; Rudolph, J.; Hindsgaul, O.; Raetz, C. R. H.; Zhou, P. Biochemistry 2005, 44, 1114.
21. McClerren, A. L.; Zhou, P.; Guan, Z.; Raetz, C. R. H.; Rudolph, J. Biochemistry 2005, 44, 1106.
22. Hernick, M.; Gennadios, H. A.; Whittington, D. A.; Rusche, K. M.; Christianson, D. W.; Fierke, C. A. J. Biol. Chem. 2005, 250, 16969.
23. Becke, A. D. J. Chem. Phys. 1993, 98, 1372.
24. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785.
25. Schrödinger, L. L. C. Jaguar 5.5 Portland, OR, 1991-2003.
26. Siegbahn, P. E. M.; Blomberg, M. R. A. Chem. Rev. 2000, 100, 421.
27. Noodleman, L.; Lovell, T.; Han, W.-G.; Li, J.; Himo, F. Chem. Rev. 2004, 104, 459.
28. Frisch, M. J. et al. Gaussian 03; Gaussian, Inc.: Pittsburgh, PA, 2004.
29. Oie, T.; Loew, G. H.; Burt, S. K.; Binkley, J. S.; MacElroy, R. D. J. Am. Chem. Soc. 1982, 104, 6169.
30. Krug, J. P.; Popelier, P. L. A.; Bader, R. F. W. J. Phys. Chem. 1992, 96, 7604.
31. Jenssen, J. H.; Baldridge, K. K.; Gordon, M. S. J. Phys. Chem. 1992, 96, 8340.
32. Antonczak, S.; Ruiz-Lopez, M. F.; Rivail, J.-L. J. Am. Chem. Soc. 1994, 116, 3912.
33. Antonczak, S.; Ruiz-Lopez, M. F.; Rivail, J.-L. J. Mol. Model. 1997, 3, 434.
34. Kallies, B.; Mitzner, R. J. Mol. Model. 1998, 4, 183.
35. Zahn, D. Eur. J. Org. Chem. 2004, 4020.
36. Gorb, L.; Asensio, A.; Tuñón, I.; Ruiz-Lopez, M. F. Chem. Eur. J. 2005, 11, 6743.
37. Gennadios, H. A.; Christianson, D. W. Biochemistry 2006, 45, 15216.
38. Hernick, M.; Fierke, C. A. Biochemistry 2006, 45, 15240.
39. Hammond, G.S.J. Am. Chem. Soc. 1955, 77, 334.
40. Pelmensehikov, V.; Blomberg, M. R. A.; Siegbahn, P. E. M. J. Biol. Inorg. Chem. 2002, 7, 284.
41. Wu, X.-H.; Quan, J.-M.; Wu, Y.-D. J. Chem. Phys. B 2007, 111, 6236.
42. Xiao, C.; Zhang, Y. J. Phys. Chem. B 2007, 111, 6229.
43. Leopoldini, M.; Russo, N.; Toscano, M. J. Phys. Chem. B 2006, 110, 1063.
44. Pelmensehikov, V.; Siegbahn, P. E. M. Inorg. Chem. 2002, 41, 5959.
45. Leopoldini, M.; Russo, N.; Toscano, M. J. Am. Chem. Soc. 2007, 129, 7776.