Structural determinants responsible for substrate recognition and mode of action in family 11 polysaccharide lyases

Journal of Biological Chemistry

Volumn 284, Issue 15, 2009, Pages 10181-10189

  Ochiai, Akihito ^a   Itoh, Takafumi ^a   Mikami, Bunzo ^a   Hashimoto, Wataru ^a   Murata, Kousaku ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID RESIDUES; BACILLUS SUBTILIS; CARBOHYDRATE-BINDING MODULES; ELIMINATION REACTION; FAMILY 11; GALACTURONIC ACIDS; GLYCOSIDE BOND; LIGAND-FREE; MODE OF ACTION; MOLECULAR CONVERSION; NON-CATALYTIC; PLANT CELL WALL; RHAMNOGALACTURONAN; SACCHARIDE MOLECULES; SEQUENCE IDENTITY; STRUCTURAL COMPARISON; STRUCTURAL DETERMINANTS; STRUCTURAL INSIGHTS; SUBSTRATE RECOGNITION; VAN DER WAALS CONTACTS;

AMINES; AMINO ACIDS; BACTERIOLOGY; ENZYMES; HYDROGEN; HYDROGEN BONDS; MOLECULES; ORGANIC ACIDS; PLANT CELL CULTURE; REACTION KINETICS; SUGARS; VAN DER WAALS FORCES;

POLYSACCHARIDES;

ASPARAGINE; ASPARTIC ACID; CARBOHYDRATE; GLYCINE; POLYMER; POLYSACCHARIDE LYASE; POLYSACCHARIDE LYASE FAMILY 11; RHAMNOSE; THREONINE; TYROSINE; UNCLASSIFIED DRUG; GLYCOSIDE; POLYSACCHARIDE;

ARTICLE; BACILLUS SUBTILIS; CONTROLLED STUDY; CRYSTALLIZATION; ENZYME ANALYSIS; ENZYME STRUCTURE; ENZYME SUBSTRATE; GEL PERMEATION CHROMATOGRAPHY; HYDROGEN BOND; MOLECULAR RECOGNITION; MUTAGENESIS; MUTANT; NONHUMAN; PRIORITY JOURNAL; PROTEIN FAMILY; X RAY DIFFRACTION; AMINO ACID SEQUENCE; CARBOHYDRATE ANALYSIS; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; ENZYME SPECIFICITY; ENZYMOLOGY; MOLECULAR GENETICS; PROTEIN BINDING; PROTEIN CONFORMATION; SEQUENCE HOMOLOGY;

BACILLUS SUBTILIS;

AMINO ACID SEQUENCE; BACILLUS SUBTILIS; CARBOHYDRATE CONFORMATION; CARBOHYDRATE SEQUENCE; GLYCOSIDES; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR SEQUENCE DATA; POLYSACCHARIDE-LYASES; POLYSACCHARIDES; PROTEIN BINDING; PROTEIN CONFORMATION; SEQUENCE HOMOLOGY, AMINO ACID; SUBSTRATE SPECIFICITY;

EID: 65649108985     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M807799200     Document Type: Article

References (44)

1. Coutinho, P. M., and Henrissat, B. (1999) Carbohydrate-active Enzymes: An Integrated Database Approach (Gilbert, H. J., Davies, G., Henrissat, B., and Svensson, B., eds) The Royal Society of Chemistry, Cambridge
2. Yoder, M. D., and Jurnak, F. (1995) Plant Physiol. 107, 349-364
3. Mayans, O., Scott, M., Connerton, I., Gravesen, T., Benen, J., Visser, J., Pickersgill, R., and Jenkins, J. (1997) Structure 5, 677-689
4. Yamasaki, M., Ogura, K., Hashimoto, W., Mikami, B., and Murata, K. (2005) J. Mol. Biol. 352, 11-21
5. Yoon, H.-J., Hashimoto, W., Miyake, O., Murata, K., and Mikami, B. (2001) J. Mol. Biol. 307, 9-16
6. Lunin, V. V., Li, Y., Linhardt, R. J., Miyazono, H., Kyogashima, M., Kaneko, T., Bell, A. W., and Cygler, M. (2004) J. Mol. Biol. 337, 367-386
7. Shaya, D., Tocilj, A., Li, Y., Myette, J., Venkataraman, G., Sasisekharan, R., and Cygler, M. (2006) J. Biol. Chem. 281, 15525-15535
8. Maruyama, Y., Hashimoto, W., Mikami, B., and Murata, K. (2005) J. Mol. Biol. 350, 974-986
9. Maruyama, Y., Mikami, B., Hashimoto, W., and Murata, K. (2007) Biochemistry 46, 781-791
10. Ogura, K., Yamasaki, M., Mikami, B., Hashimoto, W., and Murata, K. (2008) J. Mol. Biol. 380, 373-385
11. Darvill, A. G., McNeil, M., and Albersheim, P. (1978) Plant Physiol. 62, 418-422
12. Thakur, B. R., Singh, R. K., and Handa, A. K. (1997) Crit. Rev. Food Sci. Nutr. 37, 47-73
13. McNeil, M., Darvill, A. G., Fry, S. C., and Albersheim, P. (1984) Annu. Rev. Biochem. 53, 625-663
14. McNeil, M., Darvill, A. G., and Albersheim, P. (1980) Plant Physiol. 66, 1128-1134
15. O'Neill, M. A., Warrenfeltz, D., Kates, K., Pellerin, P., Doco, T., Darvill, A. G., and Albersheim, P. (1996) J. Biol. Chem. 271, 22923-22930
16. Ochiai, A., Itoh, T., Kawamata, A., Hashimoto, W., and Murata, K. (2007) Appl. Environ. Microbiol. 73, 3803-3813
17. Ochiai, A., Itoh, T., Maruyama, Y., Kawamata, A., Mikami, B., Hashimoto, W., and Murata, K. (2007) J. Biol. Chem. 282, 37134-37145
18. Shevchik, V. E., Condemine, G., Robert-Baudouy, J., and Hugouvieux-Cotte-Pattat, N. (1999) J. Bacteriol. 181, 3912-3919
19. Hashimoto, W., Miyake, O., Momma, K., Kawai, S., and Murata, K. (2000) J. Bacteriol. 182, 4572-4577
20. Bradford, M. M. (1976) Anal. Biochem. 72, 248-254
21. Ochiai, A., Yamasaki, M., Itoh, T., Mikami, B., Hashimoto, W., and Murata, K. (2006) Acta Crystallogr. F Struct. Biol. Crystalliz. Comm. 62, 438-440
22. Otwinowski, Z., and Minor, W. (1997) Methods Enzymol. 276, 307-326
23. Vagin, A., and Teplyakov, A. (1997) J. Appl. Crystallogr. 30, 1022-1025
24. Collaborative Computational Project (1994) Acta Crystallogr. Sect. D Biol. Crystallogr. 50, 760-763
25. Emsley, P., and Cowtan, K. (2004) Acta Crystallogr. Sect. D. Biol. Crystallogr. 60, 2126-2132
26. Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Acta Crystallogr. Sect. D Biol. Crystallogr. 53, 240-255
27. Kabsch, W. (1976) Acta Crystallogr. Sect. A 32, 922-923
28. Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) J. Appl. Crystallogr. 26, 283-291
29. DeLano, W. L. (2004) The PyMOL Molecular Graphics System, DeLano Scientific LLC, San Carlos, CA
30. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E. (2000) Nucleic Acids Res. 28, 235-242
31. Luzzati, V. (1952) Acta Crystallogr. 5, 802-810
32. Sibanda, B. L., and Thornton, J. M. (1985) Nature 316, 170-174
33. Ramachandran, G. N., and Sasisekharan, V. (1968) Adv. Protein Chem. 23, 283-438
34. McKie, V. A., Vincken, J. P., Voragen, A. G., van den Broek, L. A., Stimson, E., and Gilbert, H. J. (2001) Biochem. J. 355, 167-177
35. Pages, S., Valette, O., Abdou, L., Belaich, A., and Belaich, J. P. (2003) J. Bacteriol. 185, 4727-4733
36. Boraston, A. B., Bolam, D. N., Gilbert, H. J., and Davies, G. J. (2004) Biochem. J. 382, 769-781
37. Abbott, D. W., Hrynuik, S., and Boraston, A. B. (2007) J. Mol. Biol. 367, 1023-1033
38. Davies, G. J., Wilson, K. S., and Henrissat, B. (1997) Biochem. J. 321, 557-559
39. Itoh, T., Ochiai, A., Mikami, B., Hashimoto, W., and Murata, K. (2006) Biochem. Biophys. Res. Commun. 347, 1021-1029
40. Meinke, A., Damude, H. G., Tomme, P., Kwan, E., Kilburn, D. G., Miller, R. C., Jr., Warren, R. A., and Gilkes, N. R. (1995) J. Biol. Chem. 270, 4383-4386
41. 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
42. Yao, Y. Y., Shrestha, K. L., Wu, Y. J., Tasi, H. J., Chen, C. C., Yang, J. M., Ando, A., Cheng, C. Y., and Li, Y. K. (2008) Protein Eng. Des. Sel. 21, 561-566
43. Yaoi, K., Kondo, H., Hiyoshi, A., Noro, N., Sugimoto, H., Tsuda, S., Mitsuishi, Y., and Miyazaki, K. (2007) J. Mol. Biol. 370, 53-62
44. Cartmell, A., Topakas, E., Ducros, V. M., Suits, M. D., Davies, G. J., and Gilbert, H. J. (2008) J. Biol. Chem. 283, 34403-34413