What is the identity of the metal ions in the active sites of coenzyme b12-dependent diol dehydratase? a computational mutation analysis

Journal of Physical Chemistry B

Volumn 113, Issue 25, 2009, Pages 8435-8438

  Kamachi, Takashi ^a   Takahata, Masanori ^a   Toraya, Tetsuo ^b   Yoshizawa, Kazunari ^a  

^a KYUSHU UNIVERSITY   (Japan)

^b OKAYAMA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; CALCIUM; METAL IONS; METALS;

ACTIVE SITE; EXPERIMENTAL EVIDENCE; MUTATION ANALYSIS; QM/MM CALCULATIONS; SUBSTRATE-BINDING SITES;

BINDING SITES;

EID: 67649159281     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp9001737     Document Type: Article

References (62)

1. Lee, H. A., Jr.; Abeles, R. H. J. Biol. Chem. 1963, 238, 2367.
2. Zagalak, B.; Frey, P. A.; Karabatsos, G. L.; Abeles, R. H. J. Biol. Chem. 1966, 241, 3028.
3. Toraya, T.; Shirakashi, T.; Kosuga, T.; Fukui, S. Biochem. Biophys. Res. Commun. 1976, 69, 475.
4. Toraya, T. Chem. Rev. 2003, 103, 2095.
5. Toraya, T. Cell. Mol. Life Sci. 2000, 57, 106.
6. Brown, K. L. Chem. Rev. 2005, 105, 2075.
7. Banerjee, R., Ed. Chemistry and Biochemistry of B12; John Wiley &Sons: New York, 1999.
8. Dolphin, D., Ed. B12; John Wiley &Sons: New York, 1982; Vol. 2.
9. Rétey, J.; Umani-Ronchi, A.; Seibl, J.; Arigoni, D. Experientia 1966, 22, 502.
10. Rétey, J.; Umani-Ronchi, A.; Arigoni, D. Experientia 1966, 22, 72.
11. Shibata, N.; Masuda, J.; Tobimatsu, T.; Toraya, T.; Suto, K.; Morimoto, Y.; Yasuoka, N. Structure 1999, 7, 997.
12. Masuda, J.; Shibata, N.; Morimoto, Y.; Toraya, T.; Yasuoka, N. Structure 2000, 8, 775.
13. Shibata, N.; Masuda, J.; Morimoto, Y.; Yasuoka, N.; Toraya, T. Biochemistry 2002, 41, 12607.
14. Shibata, N.; Nakanishi, Y.; Fukuoka, M.; Yamanishi, M.; Yasuoka, N.; Toraya, T. J. Biol. Chem. 2003, 278, 22717.
15. Halpern, J. S.; Kim, H.; Leung, T. W. J. Am. Chem. Soc. 1984, 106, 8317.
16. Hay, B. P.; Finke, R. G. J. Am. Chem. Soc. 1986, 108, 4820.
17. Hansen, L. M.; Kumar, P. N. V. P.; Marynick, D. S. Inorg. Chem. 1994, 33, 728.
18. Hansen, L. M.; Derecskei-Kovacs, A.; Marynick, D. S. THEOCHEM 1998, 431, 53.
19. Andruniow, T.; Zgierski, M. Z.; Kozlowski, P. M. J. Phys. Chem. B 2000, 104, 10921.
20. Andruniow, T.; Zgierski, M. Z.; Kozlowski, P. M. J. Am. Chem. Soc. 2001, 123, 2679.
21. Freindorf, M.; Kozlowski, P. M. J. Am. Chem. Soc. 2004, 126, 1928.
22. Kozlowski, P. M.; Zgierski, M. Z. J. Phys. Chem. B 2004, 108, 14163.
23. Kuta, J.; Patchkovskii, S.; Zgierski, M. Z.; Kozlowski, P. M. J. Comput. Chem. 2006, 27, 1429.
24. Jensen, K. P.; Ryde, U. THEOCHEM 2002, 585, 239.
25. Jensen, K. P.; Ryde, U. J. Phys. Chem. A 2003, 107, 7539.
26. Dölker, N.; Maseras, F.; Lledós, A. J. Phys. Chem. B 2001, 105, 7564.
27. Dölker, N.; Maseras, F.; Lledós, A. J. Phys. Chem. B 2003, 107, 306.
28. Dölker, N.; Maseras, F.; Siegbahn, P. E. M. Chem. Phys. Lett. 2004, 386, 174.
29. Dölker, N.; Morreale, A.; Maseras, F. J. Biol. Inorg. Chem. 2005, 10, 509.
30. Rovira, C.; Kunc, K.; Hutter, J.; Parrinello, M. Inorg. Chem. 2001, 40, 11.
31. Jensen, K. P.; Ryde, U. J. Am. Chem. Soc. 2005, 127, 9117.
32. Kwiecien, R. A.; Khavrutskii, I. V.; Musaev, D. G.; Morokuma, K.; Banerjee, R.; Paneth, P. J. Am. Chem. Soc. 2006, 128, 1287.
33. Eda, M.; Kamachi, T.; Yoshizawa, K.; Toraya, T. Bull. Chem. Soc. Jpn. 2002, 75, 1469.
34. Toraya, T.; Eda, M.; Kamachi, T.; Yoshizawa, K. J. Biochem. (Tokyo) 2001, 130, 865.
35. Toraya, T.; Yoshizawa, K.; Eda, M.; Yamabe, T. J. Biochem. (Tokyo) 1999, 126, 650.
36. Golding, B. T.; Radom, L. J. Chem. Soc., Chem. Commun. 1973, 939.
37. Golding, B. T.; Radom, L. J. Am. Chem. Soc. 1976, 98, 6331.
38. Smith, D. M.; Golding, B. T.; Radom, L. J. Am. Chem. Soc. 1999, 121, 5700.
39. Smith, D. M.; Golding, B. T.; Radom, L. J. Am. Chem. Soc. 2001, 123, 1664.
40. Kamachi, T.; Toraya, T.; Yoshizawa, K. J. Am. Chem. Soc. 2004, 126, 16207.
41. Kamachi, T.; Toraya, T.; Yoshizawa, K. Chem.sEur. J. 2007, 13, 7864.
42. Deacon, G. B.; Delbridge, E. E.; Forsyth, C. M. Angew. Chem., Int. Ed. 1999, 38, 1766.
43. Zheng, W.; Heeg, M. J.; Winter, C. H. Eur. J. Inorg. Chem. 2004, 2652.
44. Lah, N.; Lah, J.; Zegers, I.; Wyns, L.; Messens, J. J. Biol. Chem. 2003, 278, 24673.
45. Discovery Studio 2.0 Accelrys Software Inc.: San Diego, CA, 2007.
46. Bakowies, D.; Thiel, W. J. Phys. Chem. 1996, 100, 10580.
47. ChemShell, a Computational Chemistry Shell; see www.chemshell. org.
48. Ahlrichs, R.; Bär, M.; Häser, M.; Horn, H.; Kölmel, C. Chem. Phys. Lett. 1989, 162, 165.
49. Momany, F. A.; Rone, R. J. Comput. Chem. 1992, 13, 888.
50. Momany, F. A.; Rone, R.; Kunz, H.; Frey, R. F.; Newton, S. Q.; Schäfer, L. THEOCHEM 1993, 286, 1.
51. Smith, W.; Forester, T. R. J. Mol. Graphics 1996, 14, 136.
52. Becke, A. D. Phys. Rev. A 1988, 38, 3098.
53. Becke, A. D. J. Chem. Phys. 1993, 98, 5648.
54. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785.
55. Perdew, J. P. Phys. Rev. B 1986, 33, 8822.
56. Schäfer, A.; Horn, H.; Ahlrichs, R. J. Chem. Phys. 1992, 97, 2571.
57. Schäfer, A.; Huber, C.; Ahlrichs, R. J. Chem. Phys. 1994, 100, 5829.
58. Strynadka, N. C. J.; James, M. N. G. Curr. Opin. Struct. Biol. 1991, 1, 905.
59. Toraya, T.; Sugimoto, Y.; Tamao, Y.; Shimizu, S.; Fukui, S. Biochemistry 1971, 10, 3475.
60. Manners, J. P.; Morallee, K. G.; Williams, R. J. P. J. Chem. Soc. D 1970, 965.
61. Schwartz, P.; LoBrutto, R.; Reed, G. H.; Frey, P. A. HelV. Chim. Acta 2003, 86, 3764.
62. Schwartz, P. A.; LoBrutto, R.; Reed, G. H.; Frey, P. A. Protein Sci. 2007, 16, 1157.