Crystal structure of histamine dehydrogenase from Nocardioides simplex

Journal of Biological Chemistry

Volumn 285, Issue 33, 2010, Pages 25782-25791

  Reed, Timothy ^a,b   Lushington, Gerald H ^a   Xia, Yan ^a   Hirakawa, Hidehiko ^a,c   Travis, DeAnna M ^a   Mure, Minae ^a   Scott, Emily E ^a   Limburg, Julian ^a  

^a UNIVERSITY OF KANSAS   (United States)

^b VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

^c UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITE; BINDING MODES; BINDING PROTEINS; ELECTRON-TRANSFER; FLAVIN MONONUCLEOTIDES; HISTAMINE DEHYDROGENASE; HOMODIMERS; IRON-SULFUR CLUSTERS; OXIDATIVE DEAMINATION; REDOX COFACTORS; TRIMETHYLAMINE;

ALDEHYDES; BINDING ENERGY; SULFUR;

CRYSTAL STRUCTURE;

CYSTEINYLFLAVIN MONONUCLEOTIDE; FLAVINE MONONUCLEOTIDE; FLAVOPROTEIN; HISTAMINE DEHYDROGENASE; OXIDOREDUCTASE; TRIMETHYLAMINE; TRIMETHYLAMINE DEHYDROGENASE; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CATALYSIS; CONTROLLED STUDY; CRYSTAL STRUCTURE; ELECTRON TRANSPORT; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME SPECIFICITY; METHYLOPHILUS METHYLOTROPHUS; MOLECULAR INTERACTION; MOLECULAR MODEL; NONHUMAN; OXIDATION REDUCTION REACTION; PIMELOBACTER SIMPLEX; PRIORITY JOURNAL; PROTEIN BINDING; STRUCTURE ANALYSIS;

CRYSTALLOGRAPHY, X-RAY; MOLECULAR STRUCTURE; NOCARDIACEAE; OXIDOREDUCTASES ACTING ON CH-NH GROUP DONORS; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY;

BACTERIA (MICROORGANISMS); METHYLOPHILUS METHYLOTROPHUS; PIMELOBACTER SIMPLEX;

EID: 77955476241     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M109.084301     Document Type: Article

References (70)

1. Thurmond, R. L., Gelfand, E. W., and Dunford, P. J. (2008) Nat. Rev. Drug Discov. 7, 41-53
2. Iwaki, S., Ogasawara, M., Kurita, R., Niwa, O., Tanizawa, K., Ohashi, Y., and Maeyama, K. (2002) Anal. Biochem. 304, 236-243
3. Loechel, C., Basran, A., Basran, J., Scrutton, N. S., and Hall, E. A. (2003) Analyst 128, 166-172
4. Bao, L., Sun, D., Tachikawa, H., and Davidson, V. L. (2002) Anal Chem. 74, 1144-1148
5. Siddiqui, J. A., Shoeb, S. M., Takayama, S., Shimizu, E., and Yorifuji, T. (2000) FEMS Microbiol. Lett. 189, 183-187
6. Limburg, J., Mure, M., and Klinman, J. P. (2005) Arch. Biochem. Biophys. 436, 8-22
7. Fujieda, N., Satoh, A., Tsuse, N., Kano, K., and Ikeda, T. (2004) Biochemistry 43, 10800-10808
8. Lim, L. W., Shamala, N., Mathews, F. S., Steenkamp, D. J., Hamlin, R., and Xuong, N. H. (1986) J. Biol. Chem. 261, 15140-15146
9. Hubbard, P. A., Liang, X., Schulz, H., and Kim, J. J. (2003) J. Biol. Chem. 278, 37553-37560
10. Huang, L., Rohlfs, R. J., and Hille, R. (1995) J. Biol. Chem. 270, 23958-23965
11. Steenkamp, D. J., and Beinert, H. (1982) Biochem. J. 207, 241-252
12. Fournel, A., Gambarelli, S., Guigliarelli, B., More, C., Asso, M., Chouteau, G., Hille, R., and Bertrand, P. (1998) J. Chem. Phys. 109, 10905-10913
13. Jang, M. H., Basran, J., Scrutton, N. S., and Hille, R. (1999) J. Biol. Chem. 274, 13147-13154
14. Rohlfs, R. J., Huang, L., and Hille, R. (1995) J. Biol. Chem. 270, 22196-22207
15. Roberts, P., Basran, J., Wilson, E. K., Hille, R., and Scrutton, N. S. (1999) Biochemistry 38, 14927-14940
16. Basran, J., Mewies, M., Mathews, F. S., and Scrutton, N. S. (1997) Biochemistry 36, 1989-1998
17. Scrutton, N. S., and Raine, A. R. (1996) Biochem. J. 319, 1-8
18. Binda, C., Mattevi, A., and Edmondson, D. E. (2002) J. Biol. Chem. 277, 23973-23976
19. Basran, J., Sutcliffe, M. J., and Scrutton, N. S. (2001) J. Biol. Chem. 276, 24581-24587
20. Reed, T. M., Hirakawa, H., Mure, M., Scott, E. E., and Limburg, J. (2008) Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 64, 785-787
21. Cohen, A. E., Ellis, P. J., Miller, M. D., Deacon, A. M., and Phizackerley, R. P. (2002) J. Appl. Cryst. 35, 720-726
22. Leslie, A. G. W. (2006) Acta Crystallogr. D Biol. Crystallogr. 62, 48-57
23. Collaborative Computational Project, N. (1994) Acta Crystallogr. D. Biol. Crystallogr. 50, 760-763
24. Terwilliger, T. C., and Berendzen, J. (1999) Acta Crystallogr. D Biol. Crystallogr. 55, 849-861
25. Terwilliger, T. C. (2000) Acta Crystallogr. D Biol. Crystallogr. 56, 965-972
26. McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C., and Read, R. J. (2007) J. Appl. Crystallogr. 40, 658-674
27. Matthews, B. W. (1968) J. Mol. Biol. 33, 491-497
28. Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Acta Crystallogr. D Biol. Crystallogr. 53, 240-255
29. Emsley, P., and Cowtan, K. (2004) Acta Crystallogr. D Biol. Crystallogr. 60, 2126-2132
30. Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) J. Appl. Crystallogr. 26, 283-291
31. Vriend, G. (1990) J. Mol. Graph. 8, 52-56
32. DeLano, W. L. (2002) The PyMOL Molecular Graphics System, DeLano Scientific LLC, San Carlos, CA
33. Becke, A. D. (1993) J. Chem. Phys. 98, 5648-5652
34. Lee, C., Yang, W., and Parr, R. G. (1988) Phys. Rev. B Condens. Matter 37, 785-789
35. Hehre, W. J., Ditchfield, R., and Pople, J. A. (1972) J. Chem. Phys. 56, 2257-2261
36. Clark, M., Cramer, R. D., 3rd, and Van Opdenboch, N. (1989) J. Comput. Chem. 10, 982-1012
37. Gasteiger, J., and Marsili, M. (1980) Tetrahedron 36, 3219-3228
38. Rarey, M., Wefing, S., and Lengauer, T. (1996) J. Comput. Aided Mol. Des. 10, 41-54
39. Jain, A. N. (2007) J. Comput. Aided Mol. Des. 21, 281-306
40. Dietmann, S., and Holm, L. (2001) Nat. Struct. Biol. 8, 953-957
41. Wierenga, R. K. (2001) FEBS Lett. 492, 193-198
42. Lim, L. W., Mathews, F. S., and Steenkamp, D. J. (1988) J. Biol. Chem. 263, 3075-3078
43. Trickey, P., Basran, J., Lian, L. Y., Chen, Z., Barton, J. D., Sutcliffe, M. J., Scrutton, N. S., and Mathews, F. S. (2000) Biochemistry 39, 7678-7688
44. Tsutsumi, M., Fujieda, N., Tsujimura, S., Shirai, O., and Kano, K. (2008) Biosci. Biotechnol. Biochem. 72, 786-796
45. Pace, C. P., and Stankovich, M. T. (1991) Arch. Biochem. Biophys. 287, 97-104
46. Dixon, D. A., Lindner, D. L., Branchaud, B., and Lipscomb, W. N. (1979) Biochemistry 18, 5770-5775
47. Zheng, Y. J., and Ornstein, R. L. (1996) J. Am. Chem. Soc. 118, 9402-9408
48. Basran, J., Jang, M. H., Sutcliffe, M. J., Hille, R., and Scrutton, N. S. (1999) J. Biol. Chem. 274, 13155-13161
49. Basran, J., Sutcliffe, M. J., and Scrutton, N. S. (2001) J. Biol. Chem. 276, 42887-42892
50. Mewies, M., Basran, J., Packman, L. C., Hille, R., and Scrutton, N. S. (1997) Biochemistry 36, 7162-7168
51. Leys, D., Basran, J., Talfournier, F., Sutcliffe, M. J., and Scrutton, N. S. (2003) Nat. Struct. Biol. 10, 219-225
52. Basran, J., Chohan, K. K., Sutcliffe, M. J., and Scrutton, N. S. (2000) Biochemistry 39, 9188-9200
53. Burgess, S. G., Messiha, H. L., Katona, G., Rigby, S. E., Leys, D., and Scrutton, N. S. (2008) Biochemistry 47, 5168-5181
54. Jones, M., Talfournier, F., Bobrov, A., Grossmann, J. G., Vekshin, N., Sutcliffe, M. J., and Scrutton, N. S. (2002) J. Biol. Chem. 277, 8457-8465
55. Bellamy, H. D., Lim, L. W., Mathews, F. S., and Dunham, W. R. (1989) J. Biol. Chem. 264, 11887-11892
56. Raine, A. R., Yang, C. C., Packman, L. C., White, S. A., Mathews, F. S., and Scrutton, N. S. (1995) Protein Sci. 4, 2625-2628
57. Horton, J. R., Sawada, K., Nishibori, M., Zhang, X., and Cheng, X. (2001) Structure 9, 837-849
58. Paesen, G. C., Adams, P. L., Harlos, K., Nuttall, P. A., and Stuart, D. I. (1999) Mol. Cell 3, 661-671
59. Mans, B. J., Ribeiro, J. M., and Andersen, J. F. (2008) J. Biol. Chem. 283, 18721-18733
60. Mans, B. J., Calvo, E., Ribeiro, J. M., and Andersen, J. F. (2007) J. Biol. Chem. 282, 36626-36633
61. Fukui, H., Fujimoto, K., Mizuguchi, H., Sakamoto, K., Horio, Y., Takai, S., Yamada, K., and Ito, S. (1994) Biochem. Biophys. Res. Commun. 201, 894-901
62. Gantz, I., Schäffer, M., DelValle, J., Logsdon, C., Campbell, V., Uhler, M., and Yamada, T. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 429-433
63. Lovenberg, T. W., Roland, B. L., Wilson, S. J., Jiang, X., Pyati, J., Huvar, A., Jackson, M. R., and Erlander, M. G. (1999) Mol. Pharmacol. 55, 1101-1107
64. Nakamura, T., Itadani, H., Hidaka, Y., Ohta, M., and Tanaka, K. (2000) Biochem. Biophys. Res. Commun. 279, 615-620
65. Oda, T., and Matsumoto, S. (2001) Nippon Yakurigaku Zasshi 118, 36-42
66. Jongejan, A., and Leurs, R. (2005) Arch. Pharm. 338, 248-259
67. Kelley, M. T., Bürckstümmer, T., Wenzel-Seifert, K., Dove, S., Buschauer, A., and Seifert, R. (2001) Mol. Pharmacol. 60, 1210-1225
68. Yao, B. B., Hutchins, C. W., Carr, T. L., Cassar, S., Masters, J. N., Bennani, Y. L., Esbenshade, T. A., and Hancock, A. A. (2003) Neuropharmacology 44, 773-786
69. Shin, N., Coates, E., Murgolo, N. J., Morse, K. L., Bayne, M., Strader, C. D., and Monsma, F. J., Jr. (2002) Mol. Pharmacol. 62, 38-47
70. Jongejan, A., Bruysters, M., Ballesteros, J. A., Haaksma, E., Bakker, R. A., Pardo, L., and Leurs, R. (2005) Nat. Chem. Biol. 1, 98-103