The structure of chondroitin B lyase complexed with glycosaminoglycan oligosaccharides unravels a calcium-dependent catalytic machinery

Journal of Biological Chemistry

Volumn 279, Issue 31, 2004, Pages 32882-32896

  Michel, Gurvan ^a,b,e   Pojasek, Kevin ^c   Li, Yunge ^a,b   Sulea, Traian ^a   Linhardt, Robert J ^d   Raman, Rahul ^c   Prabhakar, Vikas ^c   Sasisekharan, Ram ^c   Cygler, Miroslaw ^a,b  

^a NATIONAL RESEARCH COUNCIL CANADA   (Canada)

^b Montreal Jt Ctr for Struct Biol   (Canada)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^d RENSSELAER POLYTECHNIC INSTITUTE   (United States)

^e CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CALCIUM; CATALYSIS; COMPLEXATION; ENZYMES; OLIGOMERS; ORGANIC ACIDS; POSITIVE IONS; STRUCTURE (COMPOSITION); SUBSTRATES;

ACIDIC RESIDUES; COMPLEXES; OLIGOSACCHARIDES;

BIOCHEMISTRY;

ARGININE; CALCIUM ION; CHONDROITIN; CHONDROITIN B LYASE; CHONDROTINASE B; DERMATAN SULFATE; DISACCHARIDE; GLYCOSAMINOGLYCAN; IDURONIC ACID; LYASE; LYSINE; OLIGOSACCHARIDE; UNCLASSIFIED DRUG;

ARTICLE; CATALYSIS; COMPLEX FORMATION; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME DEGRADATION; ENZYME KINETICS; ENZYME SPECIFICITY; ENZYME STRUCTURE; FLAVOBACTERIUM; PEDOBACTER HEPARINUS; PRIORITY JOURNAL; SITE DIRECTED MUTAGENESIS;

AMINO ACID SEQUENCE; ANIMALS; ARGININE; BINDING SITES; CALCIUM; CATALYSIS; CHONDROITIN LYASES; CHONDROITINASES AND CHONDROITIN LYASES; CRYSTALLOGRAPHY, X-RAY; DERMATAN SULFATE; DISACCHARIDES; DOSE-RESPONSE RELATIONSHIP, DRUG; ELECTRONS; ELECTROPHORESIS, CAPILLARY; GLYCOSAMINOGLYCANS; IONS; KINETICS; LYSINE; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTAGENESIS; MUTAGENESIS, SITE-DIRECTED; OLIGOSACCHARIDES; POLYMERASE CHAIN REACTION; POLYSACCHARIDE-LYASES; PROTEIN CONFORMATION; SEQUENCE HOMOLOGY, AMINO ACID; SWINE;

BACTERIA (MICROORGANISMS); FLAVOBACTERIUM; PEDOBACTER; PEDOBACTER HEPARINUS;

EID: 3543011956     PISSN: 00219258     EISSN: None     Source Type: Journal    
DOI: 10.1074/jbc.M403421200     Document Type: Article

References (68)

1. Jackson, R. L., Busch, S. J., and Cardin, A. D. (1991) Physiol. Rev. 71,481-539
2. Kjellen, L., and Lindahl, U. (1991) Annu. Rev. Biochem. 60, 443-475
3. Capila, I., and Linhardt, R. J. (2002) Angew. Chem. Int. Ed. Engl. 41, 391-412
4. Ernst, S., Langer, R., Cooney, C. L., and Sasisekharan, R. (1995) Crit. Rev. Biochem. Mol. Biol. 30, 387-444
5. Sugahara, K., and Kitagawa, H. (2000) Curr. Opin. Struct. Biol. 10, 518-527
6. Valla, S., Li, J., Ertesvag, H., Barbeyron, T., and Lindahl, U. (2001) Biochimie (Paris) 83, 819-830
7. Iozzo, R. V. (1998) Annu. Rev. Biochem. 67, 609-652
8. Steyn, P. L., Segers, P., Vancanneyt, M., Sandra, P., Kersters, K., and Joubert, J. J. (1998) Int. J. Syst. Bacterial. 48, 165-177
9. Aguiar, J. A., Lima, C. R., Berto, A. G., and Michelacci, Y. M. (2003) Biotechnol. Appl. Biochem. 37, 115-127
10. Gacesa, P. (1987) FEBS Lett. 212, 199-202
11. Michelacci, Y. M., and Dietrich, C. P. (1974) Biochem. Biophys. Res. Commun. 56, 973-980
12. Michelacci, Y. M., and Dietrich, C. P. (1975) Biochem. J. 151, 121-129
13. Jandik, K. A., Gu, K., and Linhardt, R. J. (1994) Glycobiology 4, 289-296
14. Gu, K., Linhardt, R. J., Laliberte, M., and Zimmermann, J. J. (1995) Biochem. J. 312, 569-577
15. Huang, W., Matte, A., Li, Y., Kim, Y. S., Linhardt, R. J., Su, H., and Cygler, M. (1999) J. Mol. Biol. 294, 1257-1269
16. Yoder, M. D., Keen, N. T., and Jurnak, F. (1993) Science 260, 1503-1507
17. Petersen, T. N., Kauppinen, S., and Larsen, S. (1997) Structure 5, 533-544
18. Akita, M., Suzuki, A., Kobayashi, T., Ito, S., and Yamane, T. (2001) Acta Crystallogr. Sect. D Biol. Crystallogr. 57, 1786-1792
19. Michel, G., Chantalat, L., Fanchon, E., Henrissat, B., Kloareg, B., and Dideberg, O. (2001) J. Biol. Chem. 276, 40202-40209
20. Pojasek, K., Roman, R., Kiley, P., Venkataraman, G., and Sasisekharan, R. (2002) J. Biol. Chem. 277, 31179-31186
21. Pickersgill, R. W., Jenkins, J., Harris, G., Nasser, W., and Robert-Baudouy, J. (1994) Nat. Struct. Biol. 1, 717-723
22. Herren, S. R., Scavetta, R. D., Garrett, M., Legner, M., and Jurnak, F. (2003) J. Biol. Chem. 278, 12271-12277
23. Scavetta, R. D., Herron, S. R., Hotchkiss, A. T., Kita, N., Keen, N. T., Benen, J. A., Kester, H. C., Visser, J., and Jurnak, F. (1999) Plant Cell 11, 1081-1092
24. Liu, D., Shriver, Z., Godavarti, R., Venkataraman, G., and Sasisekharan, R. (1999) J. Biol. Chem. 274, 4089-4095
25. Shriver, Z., Liu, D., Hu, Y., and Sasisekharan, R. (1999) J. Biol. Chem. 274, 4082-4088
26. Huang, W., Boju, L., Tkalec, L., Su, H., Yang, H. O., Gunay, N. S., Linhardt, R. J., Kim, Y. S., Matte, A., and Cygler, M. (2001) Biochemistry 40, 2359-2372
27. Hopwood, J. J., and Elliott, H. (1981) Carbohydr. Res. 91, 165-190
28. Yang, H. O., Gunay, N. S., Toida, T., Kuberan, B., Yu, G., Kim, Y. S., and Linhardt, R. J. (2000) Glycobiology 10, 1033-1039
29. Li, Y., Matte, A., Su, H., and Cygler, M. (1999) Acta Crystallogr. Sect. D Biol. Crystallogr. 55, 1055-1057
30. Otwinowski, Z., and Minor, W. (1997) Methods Enzymol. 276, 307-326
31. Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Acta Crystallogr. Sect. D Biol. Crystallogr. 54, 905-921
32. Jones, T. A., Zhou, J. Y., Cowan, S. W., and Kjeldgaard, M. (1991) Acta Crystallogr. Sect. A 47, 110-119
33. Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) J. Appl Crystallogr. 26, 283-291
34. Tkalec, A. L., Fink, D., Blain, F., Zhang-Sun, G., Laliberte, M., Bennett, D. C., Gu, K., Zimmermann, J. J., and Su, H. (2000) Appl. Environ. Microbiol. 66, 29-35
35. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997) Nucleic Acids Res. 25, 3389-3402
36. Katoh, K., Misawa, K., Kuma, K., and Miyata, T. (2002) Nucleic Acids Res. 30, 3059-3066
37. Yoder, M. D., Lietzke, S. E., and Jurnak, F. (1993) Structure 1, 241-251
38. Pojasek, K., Shriver, Z., Kiley, P., Venkataraman, G., and Sasisekharan, R. (2001) Biochem. Biophys. Res. Commun. 286, 343-351
39. Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., and Kollman, P. A. (1995) J. Am. Chem. Soc. 117, 5179-5197
40. Woods, R. J., Dwek, R. A., Edge, C. J., and Fraser-Reid, B. (1995) J. Phys. Chem. 99, 3832-3846
41. Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., and Case, D. A. (2004) J. Comput. Chem. 25, 1157-1174
42. Cornell, W. D., Cieplak, P., Bayly, C. I., and Kollman, P. A. (1993) J. Am. Chem. Soc. 115, 9620-9631
43. Bërces, A., Whitfield, D. M., and Nukada, T. (2001) Tetrahedron 57, 477-491
44. Venkataraman, G., Sasisekharan, V., Cooney, C. L., Langer, R., and Sasisekharan, R. (1994) Proc. Natl. Acad. Sci. U. S. A. 91, 6171-6175
45. Ernst, S., Venkataraman, G., Sasisekharan, V., Langer, R., Cooney, C. L., and Sasisekharan, R. (1998) J. Am. Chem. Soc. 120, 2099-2107
46. Hepler, P. K., and Wayne, R. O. (1985) Annu. Rev. Plant. Physiol. 36, 397-439
47. Das, S. K., Mallet, J. M., Esnault, J., Driguez, P. A., Duchaussoy, P., Sizun, P., Herault, J. P., Herbert, J. M., Petitou, M., and Sinay, P. (2001) Chemistry 7, 4821-4834
48. Coutinho, P. M., and Henrissat, B. (1999) in Recent Advances in Carbohydrate Bioengineering (Gilbert, H. J., Davies, G., Henrissat, B., and Svensson, B., eds.) pp. 3-12, The Royal Society of Chemistry, Cambridge, United Kingdom
49. Howard, M. B., Ekborg, N. A., Taylor, L. E., Weiner, R. M., and Hutcheson, S. W. (2003) J. Bacteriol. 185, 3352-3360
50. Féthière, J., Eggimann, B., and Cygler, M. (1999) J. Mol. Biol. 288, 635-647
51. 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
52. Vyas, N. K., Vyas, M. N., and Quiocho, F. A. (1991) J. Biol. Chem. 266, 5226-5237
53. Shimizu, T., Nakatsu, T., Miyairi, K., Okuno, T., and Kato, H. (2002) Biochemistry 41, 6651-6659
54. Michel, G., Heibert, W., Kahn, R., Dideberg, O., and Kloareg, B. (2003) J. Mol. Biol. 334, 421-433
55. Anderson, V. E. (1998) Comprehensive Biological Catalysis: A Mechanistic Reference, Academic Press, London
56. Charnock, S. J., Brown, I. E., Turkenburg, J. P., Black, G. W., and Davies, G. J. (2002) Proc. Natl. Acad. Sci. U. S. A. 99, 12067-12072
57. Rye, C. S., and Withers, S. G. (2002) J. Org. Chem. 67, 4505-4512
58. Arnott, S., Scott, W. E., Rees, D. A., and McNab, C. G. (1974) J. Mol. Biol. 90, 253-267
59. Janaswamy, S., and Chandrasekaran, R. (2002) Carbohydr. Res. 337, 523-535
60. Manning, G. S. (1974) in Polyelectrolytes (Sélégny, E., Mandel, M., and Strauss, U., eds.) pp. 9-37, D. Riedel Publishing Co., Dordrecht-Holland, Boston
61. Steinbacher, S., Miller, S., Baxa, U., Budisa, N., Weintraub, A., Seckler, R., and Huber, R. (1997) J. Mol. Biol. 267, 865-880
62. Larsson, A. M., Andersson, R., Stahlberg, J., Kenne, L., and Jones, T. A. (2003) Structure (Camb.) 11, 1111-1121
63. Mitra, A. K., Arnott, S., Atkins, E. D., and Isaac, D. H. (1983) J. Mol. Biol. 169, 873-901
64. Wiberg, C., Heinegard, D., Wenglen, C., Timpl, R., and Morgelin, M. (2002) J. Biol. Chem. 277, 49120-49126
65. Scott, J. E. (2001) Pathol. Biol. (Paris) 49, 284-289
66. Kuwaba, K., Kobayashi, M., Nomura, Y., Irie, S., and Koyama, Y. (2002) J. Dermatol. Sci. 29, 185-194
67. Nicholls, A., Sharp, K. A., and Honig, B. (1991) Proteins Struct. Funct. Genet. 11, 281-296
68. Gouet, P., Robert, X., and Courcelle, E. (2003) Nucleic Acids Res. 31, 3320-3323