Theoretical determination of two structural forms of the active site in cadmium-containing phosphotriesterases

Journal of Physical Chemistry B

Volumn 106, Issue 3, 2002, Pages 717-722

  Zheng, Fang ^a   Zhan, Chang Guo ^b   Ornstein, Rick L ^a  

^a PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^b Columbia University ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

X-RAY CRYSTAL STRUCTURES;

CADMIUM; CRYSTAL STRUCTURE; ENZYMES; MOLECULES; POSITIVE IONS; PROBABILITY DENSITY FUNCTION; SUBSTITUTION REACTIONS; SUBSTRATES; X RAY ANALYSIS;

PHOSPHORUS COMPOUNDS;

EID: 0037165455     PISSN: 10895647     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp013064k     Document Type: Article

References (40)

1. Dumas, D.P.; Caldwell, S.R.; Wild, J.R.; Raushel, F.M. J. Biol. Chem. 1989, 264, 19659.
2. (a) Hong, S.-B.; Raushel, F.M. Biochemistry 1996, 35, 10904.
3. (b) Kuo, J.M.; Chae, M.Y.; Raushel, F.M. Biochemistry 1997, 36, 1982.
4. (c) Hong, S.-B.; Mullins, L.S.; Shim, H.; Raushel, F.M. Biochemistry 1997, 36, 9022.
5. (d) Seo, J.S.; Hynes, R.C.; Williams, D.; Chin, J. J. Am. Chem. Soc. 1998, 120, 9945.
6. (e) Hong, S.-B.; Raushel, F.M. Biochemistry 1999, 38, 1159.
7. Omburo, G.A.; Kuo, J.M.; Mullins, L.S.; Raushel, F.M. J. Biol. Chem. 1992, 267, 13278.
8. Lewis, V.E.; Donarski, W.J.; Wild, J.R.; Raushel, F.M. Biochemistry 1988, 27, 1591.
9. Chae, M.Y.; Omburo, G.A.; Kuo, J.M.; Lindahl, P.A.; Raushel, F.M. J. Am. Chem. Soc. 1993, 115, 12173.
10. Omburo, G.A.; Mullins, L.S.; Raushel, F.M. Biochemistry 1993, 32, 9148.
11. (a) Kuo, J.M.; Raushel, F.M. Biochemistry 1994, 33, 4265.
12. (b) Lai, K.; Dave, K.I.; Wild, J.R. J. Biol. Chem. 1994, 269, 16579.
13. (c) Banzon, J.A.; Kuo, J.M.; Miles, B.W.; Fischer, D.R.; Stang, P.J.; Raushel, F.M. Biochemistry 1995, 34, 743.
14. (d) Banzon, J.A.; Kuo, J.M.; Fischer, D.R.; Stang, P.J.; Raushel, F.M. Biochemistry 1995, 34, 750.
15. Benning, M.M.; Kuo, J.M.; Raushel, F.M.; Holden, H.M. Biochemistry 1994, 33, 15001.
16. Benning, M.M.; Kuo, J.M.; Raushel, F.M.; Holden, H.M. Biochemistry 1995, 34, 7973.
17. Vanhooke, J.L.; Benning, M.M.; Raushel, F.M.; Holden, H.M. Biochemistry 1996, 35, 6020.
18. Bending, M.M.; Hong, S.-B.; Raushel, F.M.; Holden, H.M. J. Biol. Chem. 2000, 275, 30556.
19. Benning, M.M.; Shim, H.; Raushel, F.M.; Holden, H.M. Biochemistry 2001, 40, 2712.
20. Zhan, C.-G.; Norberto de Souza, O.; Rittenhouse, R.; Ornstein, R.L. J. Am. Chem. Soc. 1999, 121, 7279.
21. Koca, J.; Zhan, C.-G.; Rittenhouse, R.; Ornstein, R.L. J. Am. Chem. Soc. 2001, 123, 817.
22. Kafafi, S.A.; Krauss, M. Int. J. Quantum Chem. 1999, 75, 289.
23. (a) Becke, A.D. J. Chem. Phys. 1993, 98, 5648.
24. (b) Lee, C.; Yang, W.; Parr, R.G. Phys. Rev. B 1988, 37, 785.
25. (a) Godbout, N.; Salahub, D.R.; Andzelm, J.; Wimmer, E. Can. J. Chem. 1992, 70, 560.
26. (b) Basis sets were obtained from the Extensible Computational Chemistry Environment Basis Set Database, Version 1999, as developed and distributed by the Molecular Science Computing Facility, Environmental and Molecular Sciences Laboratory, which is part of the Pacific Northwest Laboratory, P.O. Box 999, Richland, WA 99352, and funded by the U.S. Department of Energy. The Pacific Northwest Laboratory is a multi-program laboratory operated by Battelle Memorial Institue for the U.S. Department of Energy under contract DE-AC06-76RLO 1830. Contact David Feller or Karen Schuchardt for further information.
27. Schmidt, M.W.; Baldridge, K.K.; Boatz, J.A.; Elbert, S.T.; Gordon, M.S.; Jensen, J.H.; Koseki, S.; Matsunaga, N.; Nguyen, K.A.; Su, S.J.; Windus, T.L.; Dupuis, M.; Montgomery, J.A. J. Comput. Chem. 1993, 14, 1347.
28. (a) Zhan, C.-G.; Bentley, J.; Chipman, D.M. J. Chem. Phys. 1998, 108, 177.
29. (b) Zhan, C.-G.; Chipman, D.M. J. Chem. Phys. 1998, 109, 10543.
30. (c) Zhan, C.-G.; Chipman, D.M. J. Chem. Phys. 1999, 110, 1611.
31. (a) Zhan, C.-G.; Landry, D.W.; Ornstein, R.L. J. Am. Chem. Soc. 2000, 122, 2621.
32. (b) Zhan, C.-G.; Zheng, F. J. Am. Chem. Soc. 2001, 123, 2835.
33. (c) Zhan, C.-G.; Niu, S.; Ornstein, R.L. J. Chem. Soc., Perkin Trans. 2 2001, 1, 23.
34. (d) Zhan, C.-G.; Landry, D.W. J. Phys. Chem. A 2001, 105, 1296.
35. Frisch, M.J.; Trucks, G.W.; Schlegel, H.B.; Gill, P.M.W.; Johnson, B.G.; Robb, M.A.; Cheeseman, J.R.; Keith, T.; Petersson, G.A.; Montgomery, J.A.; Raghavachari, K.; Al-Laham, M.A.; Zakrzewski, V.G.; Ortiz, J.V.; Foresman, J.B.; Cioslowski, J.; Stefanov, B.B.; Nanayakkara, A.; Challacombe, M.; Peng, C.Y.; Ayala, P.Y.; Chen, W.; Wong, M.W.; Andres, J.L.; Replogle, E.S.; Gomperts, R.; Martin, R.L.; Fox, D.J.; Binkley, J.S.; Defrees, D.J.; Baker, J.; Stewart, J.P.; Head-Gordon, M.; Gonzalez, C.; Pople, J.A. Gaussian 94, Revision D.1; Gaussian, Inc., Pittsburgh, PA, 1995.
36. Frisch, M.J.; Tracks, G.W.; Schlegel, H.B.; Scuseria, G.E.; Robb, M.A.; Cheeseman, J.R.; Zakrzewski, V.G.; Montgomery, J.A.; Stratmann, R.E.; Burant, J.C.; Dapprich, S.; Millam, J.M.; Daniels, A.D.; Kudin, K.N.; Strain, M.C.; Farkas, O.; Tomasi, J.; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G.A.; Ayala, P.Y.; Cui, Q.; Morokuma, K.; Malick, D.K.; Rabuck, A.D.; Raghavachari, K.; Foresman, J.B.; Cioslowski, J.; Ortiz, J.V.; Stefanov, B.B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Gomperts, R.; Martin, R.L.; Fox, D.J.; Keith, T.; Al-Laham, M.A.; Peng, C.Y.; Nanayakkara, A.; Gonzalez, C.; Challacombe, M.; Gill, P.M.W.; Johnson, B.; Chen, W.; Wong, M.W.; Andres, J.L.; Gonzalez, A.C.; Head-Gordon, M.; Replogle, E.S.; Pople, J.A. Gaussian 98, Revision A.6; Gaussian, Inc., Pittsburgh, PA, 1998.
37. CRC Handbook of Chemistry and Physics, 76th ed.; Lide, D.R., Ed.; CRC Press: New York, 1996.
38. 2+-substituted PTE. In addition, the calculated free energies of models 2 and 2a so close that both had chances to exist in the crystal depending on the condition of crystal growth. Assuming that the reported crystal existed in the structural form like model 2a, the second bridging ligand may be regarded as a hydroxide plus a water molecule which strongly hydrogen-bonds to the hydroxide. When the bridging hydroxide plus a water molecule hydrogen-bonded to the hydroxide is modeled as a simple hydroxide (or water), its position is expected to be an average of the real hydroxide and the real water molecule. According to this assumption, the average distance between the second bridging ligand and the two cadmiun ions in model 2a should be ∼3.03 Å compared to the corresponding average value, ∼2.26 Å, for model 2. Further assuming that the reported crystal is close to a simple 1:1 mixture of two structural forms such as models 2 and 2a, the average distance between the second bridging ligand and the two cadmiun ions should be close to ∼2.65 Å which is in excellent agreement with the experimental value of ∼2.7 Å.
39. Lim, C.; Bashford, D.; Karplus, M. J. Phys. Chem. 1991, 95, 5610.
40. Dumas, D.P.; Raushel, F.M. J. Biol. Chem. 1990, 265, 21498.