Crystal structure of an exo-1,5-α-L-arabinofuranosidase from Streptomyces avermitilis provides insights into the mechanism of substrate discrimination between exo- and endo-type enzymes in glycoside hydrolase family 43

Journal of Biological Chemistry

Volumn 285, Issue 44, 2010, Pages 34134-34143

  Fujimoto, Zui ^a   Ichinose, Hitomi ^b   Maehara, Tomoko ^b   Honda, Mariko ^b   Kitaoka, Motomitsu ^b   Kaneko, Satoshi ^b  

^a NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

^b NATIONAL FOOD RESEARCH INSTITUTE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ARABINAN BINDING MODULE; ARABINANS; CARBOHYDRATE BINDING MODULE FAMILY 42; CARBOHYDRATE BINDING MODULES; CATALYTIC DOMAINS; CATALYTIC MODULES; COMPLEX STRUCTURE; GLYCOSIDE HYDROLASE FAMILY 43; LOOP REGIONS; POCKET STRUCTURES; SIDE CHAINS; STREPTOMYCES AVERMITILIS; SUB-DOMAINS; SUBSITES; SUBSTRATE DISCRIMINATION; SUBSTRATE SPECIFICITY; SUBSTRATE-BINDING;

BINDING ENERGY; BINDING SITES; BIOCHEMISTRY; CARBOHYDRATES; CATALYSTS; ENZYMES; SUBSTRATES; SUGAR (SUCROSE);

CRYSTAL STRUCTURE;

ALPHA ARABINOFURANOSIDASE; EXO 1,5 ALPHA ARABINOFURANOSIDASE; GLYCOSIDASE; GLYCOSIDE HYDROLASE 43; UNCLASSIFIED DRUG;

ARTICLE; BETA SHEET; CARBOHYDRATE ANALYSIS; CARBOXY TERMINAL SEQUENCE; CATALYSIS; COMPLEX FORMATION; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME ACTIVITY; ENZYME SPECIFICITY; MUTAGENESIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DETERMINATION; PROTEIN DOMAIN; PROTEIN FOLDING; STREPTOMYCES; STREPTOMYCES AVERMITILIS; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; ARGININE; BINDING SITES; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; GLYCOSIDE HYDROLASES; MOLECULAR SEQUENCE DATA; MUTAGENESIS; MUTATION; PROTEIN BINDING; PROTEIN CONFORMATION; SEQUENCE HOMOLOGY, AMINO ACID; STREPTOMYCES; SUBSTRATE SPECIFICITY; TYROSINE;

LOTUS; STREPTOMYCES AVERMITILIS;

EID: 77958582059     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M110.164251     Document Type: Article

References (40)

1. Carpita, N. C., and Gibeaut, D. M. (1993) Plant J. 3, 1-30
2. Saha, B. C. (2003) J. Ind. Microbiol. Biotechnol. 30, 279-291
3. Aristidou, A., and Penttilä, M. (2000) Curr. Opin. Biotechnol. 11, 187-198
4. Skoog, K., and Hahn-Hägerdal, B. (1988) Enzyme Microb. Technol. 10, 66-80
5. Seri, K., Sanai, K., Matsuo, N., Kawakubo, K., Xue, C., and Inoue, S. (1996) Metabolism 45, 1368-1374
6. Sanai, K., Seri, K., and Inoue, S. (1997) J. Jpn. Soc. Nutr. Food Sci. 50, 133-137
7. Osaki, S., Kimura, T., Sugimoto, T., Hizukuri, S., and Iritani, N. (2001) J. Nutr. 131, 796-799
8. Kaneko, S., Shimasaki, T., and Kusakabe, I. (1993) Biosci. Biotechnol. Biochem. 57, 1161-1165
9. Kaneko, S., Sano, M., and Kusakabe, I. (1994) Appl. Environ. Microbiol. 60, 3425-3428
10. Kaneko, S., and Kusakabe, I. (1995) Biosci. Biotechnol. Biochem. 59, 2132-2133
11. Kaneko, S., Kuno, A., Matsuo, N., Ishii, T., Kobayashi, H., Hayashi, K., and Kusakabe, I. (1998) Biosci. Biotechnol. Biochem. 62, 2205-2210
12. Kaneko, S., Higashi, K., Yasui, T., and Kusakabe, I. (1998) J. Ferment. Bioeng. 85, 518-520
13. Kaneko, S., Arimoto, M., Ohba, M., Kobayashi, H., Ishii, T., and Kusakabe, I. (1998) Appl. Environ. Microbiol. 64, 4021-4027
14. Kaneko, S., Ishii, T., Kobayashi, H., and Kusakabe, I. (1998) Biosci. Biotechnol. Biochem. 62, 695-699
15. Matsuo, N., Kaneko, S., Kuno, A., Kobayashi, H., and Kusakabe, I. (2000) Biochem. J. 346, 9-15
16. Henrissat, B. (1991) Biochem. J. 280, 309-316
17. Cantarel, B. L., Coutinho, P. M., Rancurel, C., Bernard, T., Lombard, V., and Henrissat, B. (2009) Nucleic Acids Res. 37, D233-D238
18. Ichinose, H., Yoshida, M., Fujimoto, Z., and Kaneko, S. (2008) Appl. Microbiol. Biotechnol. 80, 399-408
19. Miyanaga, A., Koseki, T., Matsuzawa, H., Wakagi, T., Shoun, H., and Fushinobu, S. (2004) J. Biol. Chem. 279, 44907-44914
20. Miyanaga, A., Koseki, T., Miwa, Y., Mese, Y., Nakamura, S., Kuno, A., Hirabayashi, J., Matsuzawa, H., Wakagi, T., Shoun, H., and Fushinobu, S. (2006) Biochem. J. 399, 503-511
21. Fujimoto, Z., Ichinose, H., and Kaneko, S. (2008) Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 64, 1007-1009
22. Kawabata, Y., Kaneko, S., Kusakabe, I., and Gama, Y. (1995) Carbohydr. Res. 267, 39-47
23. Berlin, W., and Sauer, B. (1996) Anal. Biochem. 243, 171-175
24. Otwinowski, Z., and Minor, W. (1997) Methods Enzymol. 276, 307-326
25. Terwilliger, T. C. (2003) Methods Enzymol. 374, 22-37
26. Emsley, P., and Cowtan, K. (2004) Acta Crystallogr. D Biol. Crystallogr. 60, 2126-2132
27. Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Acta Crystallogr. D Biol. Crystallogr. 53, 240-255
28. Ichinose, H., Yoshida, M., Kotake, T., Kuno, A., Igarashi, K., Tsumuraya, Y., Samejima, M., Hirabayashi, J., Kobayashi, H., and Kaneko, S. (2005) J. Biol. Chem. 280, 25820-25829
29. Beisel, H. G., Kawabata, S., Iwanaga, S., Huber, R., and Bode, W. (1999) EMBO J. 18, 2313-2322
30. Murzin, A. G., Lesk, A. M., and Chothia, C. (1992) J. Mol. Biol. 223, 531-543
31. Ichinose, H., Fujimoto, Z., Honda, M., Harazono, K., Nishimoto, Y., Uzura, A., and Kaneko, S. (2009) J. Biol. Chem. 284, 25097-25106
32. Fujimoto, Z., Kuno, A., Kaneko, S., Kobayashi, H., Kusakabe, I., and Mizuno, H. (2002) J. Mol. Biol. 316, 65-78
33. Nurizzo, D., Turkenburg, J. P., Charnock, S. J., Roberts, S. M., Dodson, E. J., McKie, V. A., Taylor, E. J., Gilbert, H. J., and Davies, G. J. (2002) Nat. Struct. Biol. 9, 665-668
34. Brüx, C., Ben-David, A., Shallom-Shezifi, D., Leon, M., Niefind, K., Shoham, G., Shoham, Y., and Schomburg, D. (2006) J. Mol. Biol. 359, 97-109
35. Proctor, M. R., Taylor, E. J., Nurizzo, D., Turkenburg, J. P., Lloyd, R. M., Vardakou, M., Davies, G. J., and Gilbert, H. J. (2005) Proc. Natl. Acad. Sci. U.S.A. 102, 2697-2702
36. Vandermarliere, E., Bourgois, T. M., Winn, M. D., van Campenhout, S., Volckaert, G., Delcour, J. A., Strelkov, S. V., Rabijns, A., and Courtin, C. M. (2009) Biochem. J. 418, 39-47
37. Pitson, S. M., Voragen, A. G., and Beldman, G. (1996) FEBS Lett. 398, 7-11
38. Shallom, D., Leon, M., Bravman, T., Ben-David, A., Zaide, G., Belakhov, V., Shoham, G., Schomburg, D., Baasov, T., and Shoham, Y. (2005) Biochemistry 44, 387-397
39. Kabsch, W., and Sander, C. (1983) Biopolymers 22, 2577-2637
40. Wallace, A. C., Laskowski, R. A., and Thornton, J. M. (1995) Protein Eng. 8, 127-134