From lipid transport to oxygenation of aromatic compounds: Evolution within the bet v1-like superfamily

Journal of Biomolecular Structure and Dynamics

Volumn 29, Issue 1, 2011, Pages 67-78

  Chakraborty, Joydeep ^a   Dutta, Tapan K ^a  

^a BOSE INSTITUTE   (India)

Author keywords

Aromatic ring hydroxylating oxygenase; Bet v1 like superfamily; Iron sulfur protein; Rieske protein; Structural evolution

Indexed keywords

AROMATIC COMPOUND; BACTERIAL ENZYME; BET V1 LIKE SUPERFAMILY PROTEIN; IRON SULFUR PROTEIN; POLLEN ANTIGEN; RING HYDROXYLATING OXYGENASE; UNCLASSIFIED DRUG;

ALPHA CHAIN; ARTICLE; CONTROLLED STUDY; ENZYME ACTIVE SITE; ENZYME SUBUNIT; LIPID TRANSPORT; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; OXYGENATION; PRIORITY JOURNAL; PROTEIN MODIFICATION; PROTEIN STRUCTURE; STRUCTURAL HOMOLOGY; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS; TAXONOMY;

EID: 79959435267     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2011.10507375     Document Type: Article

References (63)

1. Resnick, S. M., Lee, K., and Gibson, D. T., 1996. J Ind Microbiol, 17:438–457.
2. Peng, R-H., Xiong, A-S., Xue, Y., Fu, X-Y., Gao, F., Zhao, W., Tian, Y-S., and Yao, Q-H., 2008. FEMS Microbiol. Rev, 32:927–955.
3. Guo, F. B., and Lin, Y., 2009. J Biomol Struct Dyn, 26:413–420.
4. Cho, I. H., Lu, Z. R., Yu, J. R., Park, Y. D., Yang, J. M., Hahn, M. J., and Zou, F., 2009. J Biomol Struct Dyn, 27:331–345.
5. Sabbia, V., Romero, H., Musto, H., and Naya, H., 2009. J Biomol Struct Dyn, 27:361–369.
6. Zhao, J. N., Wang, Y., Zhao, B. S., and Chen, L. L., 2009. J Biomol Struct Dyn, 27:371–380.
7. Mukhopadhyay, P., and Ghosh, T. C., 2010. J Biomol Struct Dyn, 27:477–488.
8. Anbazhagan, P., Purushottam, M., Kumar, H. B. K., Mukherjee, O., Jain, S., and Sowdhamini, R., 2010. J Biomol Struct Dyn, 27:581–598.
9. Putta, P., and Mitra, C. K., 2010. J Biomol Struct Dyn, 27:599–610.
10. Liu, Z., Xu, Y., Wu, L., and Zhang, S., 2010. J Biomol Struct Dyn, 28:97–106.
11. Lu, Z. R., Seo, E., Yan, L., Yin, S. J., Si, Y. X., Qian, G. Y., Park, Y. D., and Yang, J. M., 2010. J Biomol Struct Dyn, 28:259–276.
12. Das, S., Mitra, S., and Chakrabarti, J., 2010. J Biomol Struct Dyn, 28:239–246.
13. Das, S., Mukherjee, R., Sahoo, S., Thakkar, R., and Chakrabarti, J., 2009. J Biomol Struct Dyn, 27:381–390.
14. Zhang, S., and Wang, T., 2010. J Biomol Struct Dyn, 28:247–258.
15. Huang, W., Guo, Y., and Zhang, J., 2009. J Biomol Struct Dyn, 26:599–608.
16. Jia, C., Liu, T., Zhang, X., Fu, H., and Yang, Q., 2009. J Biomol Struct Dyn, 26:763–769.
17. Sujatha, K., Mahalakshmi, A., Solaiman, D. K. Y., and Shenbagarathai, R., 2009. J Biomol Struct Dyn, 26:771–779.
18. Murzin, A. G., Brenner, S. E., Hubbard, T., and Chothia, C., 1995. J Mol Biol, 247:536–540.
19. Breiteneder, H., Pettenburger, K., Bito, A., Valenta, R., Kraft, D., Rumpold, H., Scheiner, O., and Breitenbach, M., 1989. EMBO J, 8:1935–1938.
20. van Loon, L. C., Rep, M., and Pieterse, C. M., 2006. Annu Rev Phytopathol, 44:135–162.
21. Radauer, C., Lackner, P., and Breiteneder, H., 2008. BMC Evol Biol, 8:286
22. Gajhede, M., and et al. 1996. Nat Struct Biol, 3:1040–1045.
23. Rieske, J. S., MacLennan, D. H., and Coleman, R., 1964. Biochem Biophys Res Commun, 15:338–344.
24. Schneider, D., and Schmidt, C. L., 2005. Biochimica et Biophysica Acta, 1710:1–12.
25. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E., 2000. Nucleic Acid Res, 28:235–242.
26. Brenner, S. E., Koehl, P., and Levitt, M., 2000. Nucleic Acid Res, 28:254–256.
27. Gibrat, J. F., Madej, T., and Bryant, S. H., 1996. Curr Opin Struct Biol, 6:377–385.
28. Russell, R. B., and Barton, G. J., 1992. Proteins, 14:309–323.
29. Humphrey, W., Dalke, A., and Schulten, K., 1996. J Mol Graph, 14:33–38.
30. Eargle, J., Wright, D., and Luthey-Schulten, Z., 2006. Bioinformatics, 22:504–506.
31. Panchenko, A. R., and Madej, T., 2004. Proteins, 57:539–547.
32. O'Donoghue, P., and Luthey-Schulten, Z., 2005. J Mol Biol, 346:875–894.
33. Holm, L., and Sander, C., 1993. J Mol Biol, 233:123–138.
34. Fitch, W. M., and Margoliash, E., 1967. Science, 155:279–284.
35. Felsenstein, J., 1989. Cladistics, 5:164–166.
36. Tamura, K., Dudley, J., Nei, M., and Kumar, S., 2007. Mol Biol Evol, 24:1596–1599.
37. Johnson, M. S., Sutcliffe, M. J., and Blundell, T. L., 1990. J Mol Evol, 30:43–59.
38. Johnson, M. S., Sali, A., and Blundell, T. L., 1992. Methods Enzymol, 183:670–690.
39. Marchler-Bauer, A., Panchenko, A., Shoemaker, B., Thiessen, P., Geer, L., and Bryant, S., 2002. Nucleic Acid Res, 30:281–283.
40. Ptitsyn, O. B., and Finkelstein, A. V., 1981. Q Rev Biophys, 13:339–386.
41. Holm, L., and Sander, C., 1997. Proc Int Conf Intell Syst Mol Biol, 5:140–146.
42. Russell, R. B., Saqi, M. A., Sayle, R. A., Bates, P. A., and Sternberg, M. J., 1997. J Mol Biol, 269:423–439.
43. Lupas, A. N., Ponting, C. P., and Russell, R. B., 2001. J Struct Biol, 134:191–203.
44. Chothia, C., and Lesk, A. M., 1986. EMBO J, 5:823–826.
45. Holm, L., and Sander, C., 1996. Science, 273:595–603.
46. Grishin, N. V., 2001. J Str Biol, 134:167–185.
47. Illergard, K., Ardell, D. H., and Elofsson, A., 2009. Proteins, 77:499–508.
48. Todd, A. E., Orengo, C. A., and Thornton, J. M., 2001. J Mol Biol, 307:1113–1143.
49. Todd, A. E., Orengo, C. A., and Thornton, J. M., 2002. Structure, 10:1435–1451.
50. Murzin, A. G., 1998. Curr Opin Struct Biol, 8:380–387.
51. Matsuo, Y., and Bryant, S. H., 1999. Proteins, 35:70–79.
52. Kinch, L. N., and Grishin, N. V., 2002. Curr Opin Struct Biol, 12:400–408.
53. Matthews, B., 1995. Adv Protein Chem, 46:249–278.
54. Berezovsky, I. N., Grosberg, A. Y., and Trifonov, E. N., 2000. FEBS Lett, 466:283–286.
55. Berezovsky, I. N., and Trifonov, E. N., 2001. J Biomol Struct Dyn, 19:397–403.
56. Berezovsky, I. N., and Trifonov, E. N., 2001. J Mol Biol, 307:1419–1426.
57. Berezovsky, I. N., Kirzhner, V. M., Kirzhner, A., Rosenfeld, V. R., and Trifonov, E. N., 2003. J Biomol Struct Dyn, 21:317–325.
58. Berezovsky, I. N., Kirzhner, A., Kirzhner, V. M., and Trifonov, E. N., 2003. J Biomol Struct Dyn, 21:327–339.
59. Goncearenco, A., and Berezovsky, I. N., 2010. Bioinformatics, 26:i497–503.
60. Capyk, J. K., D'Angelo, I., Strynadka, N. C., and Eltis, L. D., 2009. J Biol Chem, 284:9937–9946.
61. Pandey, A. K., and Sassetti, C. M., 2008. Proc Natl Acad Sci, 105:4376–4380.
62. Yam, K. C., and et al. 2009. PLoS Pathog., 5:e1000344
63. Kauppi, B., Lee, K., Carredano, E., Parales, R. E., Gibson, D. T., Eklund, H., and Ramaswamy, S., 1998. Structure, 6:571–586.