X-ray crystallographic studies of family 11 xylanase Michaelis and product complexes: Implications for the catalytic mechanism

Acta Crystallographica Section D: Biological Crystallography

Volumn 70, Issue 1, 2014, Pages 11-23

  Wan, Qun ^a,b   Zhang, Qiu ^a   Hamilton Brehm, Scott ^a   Weiss, Kevin ^a   Mustyakimov, Marat ^a   Coates, Leighton ^a   Langan, Paul ^a   Graham, David ^a   Kovalevsky, Andrey ^a  

^a OAK RIDGE NATIONAL LABORATORY   (United States)

^b YANGZHOU UNIVERSITY   (China)

Author keywords

catalytic mechanism; family 11 xylanase; glycoside hydrolase; ligand binding; mutagenesis; Trichoderma reesei

Indexed keywords

ENDO 1,4 BETA XYLANASE; GLYCOSIDASE; TRISACCHARIDE; XYLOTRIOSE;

ARTICLE; BINDING SITE; BIOCATALYSIS; CATALYTIC MECHANISM; CHEMICAL STRUCTURE; CHEMISTRY; ENZYME SPECIFICITY; ENZYMOLOGY; FAMILY 11 XYLANASE; GENETICS; HYPOCREA JECORINA; LIGAND BINDING; METABOLISM; MUTAGENESIS; TRICHODERMA; X RAY CRYSTALLOGRAPHY;

CATALYTIC MECHANISM; FAMILY 11 XYLANASE; GLYCOSIDE HYDROLASE; LIGAND BINDING; MUTAGENESIS; TRICHODERMA REESEI;

BINDING SITES; BIOCATALYSIS; CRYSTALLOGRAPHY, X-RAY; ENDO-1,4-BETA XYLANASES; MODELS, MOLECULAR; MUTAGENESIS; SUBSTRATE SPECIFICITY; TRICHODERMA; TRISACCHARIDES;

EID: 84892416888     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S1399004713023626     Document Type: Article

References (63)

1. Adams, P. D. et al. (2010). Acta Cryst. D66, 213-221.
2. Afonine, P. V., Grosse-Kunstleve, R. W., Echols, N., Headd, J. J., Moriarty, N. W., Mustyakimov, M., Terwilliger, T. C., Urzhumtsev, A., Zwart, P. H. & Adams, P. D. (2012). Acta Cryst. D68, 352-367.
3. Bailey, M. J., Biely, P. & Poutanen, K. (1992). J. Biotechnol. 23, 257-270.
4. Biarnés, X., Ardévol, A., Planas, A. & Rovira, C. (2010). Biocatal. Biotransform. 28, 33-40.
5. Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S. & Richardson, D. C. (2010). Acta Cryst. D66, 12-21.
6. Collins, T., Gerday, C. & Feller, G. (2005). FEMS Microbiol. Rev. 29, 3-23.
7. Davies, G. J., Ducros, V. M., Varrot, A. & Zechel, D. L. (2003). Biochem. Soc. Trans. 31, 523-527.
8. Davies, G. & Henrissat, B. (1995). Structure, 3, 853-859.
9. Davies, G. J., Planas, A. & Rovira, C. (2012). Acc. Chem. Res. 45, 308-316.
10. Davies, G. J., Wilson, K. S. & Henrissat, B. (1997). Biochem. J. 321, 557-559.
11. Davoodi, J., Wakarchuk, W. W., Campbell, R. L., Carey, P. R. & Surewicz, W. K. (1995). Eur. J. Biochem. 232, 839-843.
12. De Vos, D., Collins, T., Nerinckx, W., Savvides, S. N., Claeyssens, M., Gerday, C., Feller, G. & Van Beeumen, J. (2006). Biochemistry, 45, 4797-4807.
13. Dodd, D. & Cann, I. K. O. (2009). Glob. Change Biol. Bioenerg. 1, 2-17.
14. Drevland, R. M., Waheed, A. & Graham, D. E. (2007). J. Bacteriol. 189, 4391-4400.
15. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. (2010). Acta Cryst. D66, 486-501.
16. Fushinobu, S., Ito, K., Konno,M.,Wakagi, T. &Matsuzawa, H. (1998). Protein Eng. 11, 1121-1128.
17. Gaaaab, J., John, H., Melzer, M. & Blum, M. (2010). J. Chromatogr. B, 878, 1382-1390.
18. Garlock, R. J., Chundawat, S. P., Balan, V. & Dale, B. E. (2009). Biotechnol. Biofuels, 2, 29.
19. Gibbs, M., Reeves, R., Hardiman, E., Choudhary, P., Daniel, R. & Bergquist, P. (2010). New Biotechnol. 27, 795-802.
20. Gupta, R., Kim, T. H. & Lee, Y. Y. (2008). Appl. Biochem. Biotechnol. 148, 59-70.
21. Havukainen, R., Törrönen, A., Laitinen, T. & Rouvinen, J. (1996). Biochemistry, 35, 9617-9624.
22. Jänis, J., Pulkkinen, P., Rouvinen, J. & Vainiotalo, P. (2007). Anal. Biochem. 365, 165-173.
23. Jeffrey, G. A. & Yates, J. H. (1979). Carbohydr. Res. 74, 319-322.
24. Joshi, M. D., Sidhu, G., Pot, I., Brayer, G. D., Withers, S. G. & McIntosh, L. P. (2000). J. Mol. Biol. 299, 255-279.
25. Kamata, K., Mitsuya, M., Nishimura, T., Eiki, J. & Nagata, Y. (2004). Structure, 12, 429-438.
26. Ko, E. P., Akatsuka, H., Moriyama, H., Shinmyo, A., Hata, Y., Katsube, Y., Urabe, I. & Okada, H. (1992). Biochem. J. 288, 117-121.
27. Krissinel, E. & Henrick, K. (2004). Acta Cryst. D60, 2256-2268.
28. Liu, J., Zhang, C. & Xu, D. (2012). J. Mol. Graph. Model. 37, 67-76.
29. Ludwiczek, M. L., D'Angelo, I., Yalloway, G. N., Brockerman, J. A., Okon, M., Nielsen, J. E., Strynadka, N. C., Withers, S. G. & McIntosh, L. P. (2013). Biochemistry, 52, 3138-3156.
30. Ludwiczek, M. L., Heller, M., Kantner, T. & McIntosh, L. P. (2007). J. Mol. Biol. 373, 337-354.
31. McCarter, J. D. & Withers, S. G. (1994). Curr. Opin. Struct. Biol. 4, 885-892.
32. McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C. & Read, R. J. (2007). J. Appl. Cryst. 40, 658-674.
33. McIntosh, L. P., Hand, G., Johnson, P. E., Joshi, M. D., Körner, M., Plesniak, L. A., Ziser, L., Wakarchuk, W. W. & Withers, S. G. (1996). Biochemistry, 35, 9958-9966.
34. Miao, S., Ziser, L., Aebersold, R. & Withers, S. G. (1994). Biochemistry, 33, 7027-7032.
35. Nerinckx, W., Desmet, T. & Claeyssens, M. (2006). ARKIVOC, 2006, 90-116.
36. Notenboom, V., Birsan, C., Nitz, M., Rose, D. R., Warren, R. A. J. & Withers, S. G. (1998). Nature Struct. Mol. Biol. 5, 812-818.
37. Notenboom, V., Birsan, C., Warren, R. A. J., Withers, S. G. & Rose, D. R. (1998). Biochemistry, 37, 4751-4758.
38. Otwinowski, Z. & Minor,W. (1997). Methods Enzymol. 276, 307-326.
39. Porter, C. M. & Miller, B. G. (2012). Bioorg. Chem. 43, 44-50.
40. Rantwijk, F. van, Woudenberg-van Oosterom, M. & Sheldon, R. (1999). J. Mol. Catal. B Enzym. 6, 511-532.
41. Sabini, E., Sulzenbacher, G., Dauter, M., Dauter, Z., Jørgensen, P. L., Schülein, M., Dupont, C., Davies, G. J. & Wilson, K. S. (1999). Chem. Biol. 6, 483-492.
42. Sabini, E., Wilson, K. S., Danielsen, S., Schülein, M. & Davies, G. J. (2001). Acta Cryst. D57, 1344-1347.
43. Saff, E. B. & Kuijlaars, A. B. J. (1997). Math. Intell. 19, 5-11.
44. Scheller, H. V. & Ulvskov, P. (2010). Annu. Rev. Plant Biol. 61, 263-289.
45. Sidhu, G., Withers, S. G., Nguyen, N. T., McIntosh, L. P., Ziser, L. & Brayer, G. D. (1999). Biochemistry, 38, 5346-5354.
46. Strynadka, N. C. & James, M. N. G. (1996). EXS, 75, 185-222.
47. Suzuki, R., Fujimoto, Z., Ito, S., Kawahara, S., Kaneko, S., Taira, K., Hasegawa, T. & Kuno, A. (2009). J. Biochem. 146, 61-70.
48. Taguchi, H., Hamasaki, T., Akamatsu, T. & Okada, H. (1996). Biosci. Biotechnol. Biochem. 60, 983-985.
49. Törnkvist, M., Larsson, G. & Enfors, S-O. (1996). Bioprocess Biosyst. Eng. 15, 231-237.
50. Törrönen, A., Harkki, A. & Rouvinen, J. (1994). EMBO J. 13, 2493- 2501.
51. Törrönen, A., Mach, R. L., Messner, R., Gonzalez, R., Kalkkinen, N., Harkki, A. & Kubicek, C. P. (1992). Nature Biotechnol. 10, 1461- 1465.
52. Törrönen, A. & Rouvinen, J. (1995). Biochemistry, 34, 847-856.
53. Törrönen, A. & Rouvinen, J. (1997). J. Biotechnol. 57, 137-149.
54. Vandermarliere, E., Bourgois, T. M., Rombouts, S., Van Campenhout, S., Volckaert, G., Strelkov, S. V., Delcour, J. A., Rabijns, A. & Courtin, C. M. (2008). Biochem. J. 410, 71-79.
55. Vardakou, M., Dumon, C., Murray, J.W., Christakopoulos, P.,Weiner, D. P., Juge, N., Lewis, R. J., Gilbert, H. J. & Flint, J. E. (2008). J. Mol. Biol. 375, 1293-1305.
56. Vasella, A., Davies, G. J. & Boooohm, M. (2002). Curr. Opin. Chem. Biol. 6, 619-629.
57. Wakarchuk, W. W., Campbell, R. L., Sung, W. L., Davoodi, J. & Yaguchi, M. (1994). Protein Sci. 3, 467-475.
58. Wan, Q., Kovalevsky, A., Zhang, Q., Hamilton-Brehm, S., Upton, R., Weiss, K. L., Mustyakimov,M., Graham, D., Coates, L. & Langan, P. (2013). Acta Cryst. F69, 320-323.
59. Watanabe, N., Akiba, T., Kanai, R. & Harata, K. (2006). Acta Cryst. D62, 784-792.
60. White, A. & Rose, D. R. (1997). Curr. Opin. Struct. Biol. 7, 645-651.
61. Winn, M. D. et al. (2011). Acta Cryst. D67, 235-242.
62. Zechel, D. L. & Withers, S. G. (2000). Acc. Chem. Res. 33, 11-18.
63. Zolotnitsky, G., Cogan, U., Adir, N., Solomon, V., Shoham, G. & Shoham, Y. (2004). Proc. Natl Acad. Sci. USA, 101, 11275-11280.