Structural snapshots of heparin depolymerization by heparin lyase I

Journal of Biological Chemistry

Volumn 284, Issue 49, 2009, Pages 34019-34027

  Han, Young Hyun ^a,b   Garron, Marie Line ^c   Kim, Hye Yeon ^a   Kim, Wan Seok ^d   Zhang, Zhenqing ^e   Ryu, Kyeong Seok ^a   Shaya, David ^c   Xiao, Zhongping ^e   Cheong, Chaejoon ^a   Kim, Yeong Shik ^d   Linhardt, R J ^e   Jeon, Young Ho ^a,f   Cygler, Miroslaw ^c,g  

^a Korea Basic Science Institute (KBSI)   (South Korea)

^b Chungbuk National University   (South Korea)

^c MCGILL UNIVERSITY   (Canada)

^d Seoul National University   (South Korea)

^e Research Rensselaer Polytechnic Institute   (United States)

^f University of Science and Technology (UST)   (South Korea)

^g NATIONAL RESEARCH COUNCIL CANADA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGOSACCHARIDES;

BACTEROIDES THETAIOTAOMICRON; CATALYTIC MECHANISMS; GLYCOSIDIC LINKAGES; KINETIC ANALYSIS; STRUCTURAL SIMILARITY; STRUCTURAL SNAPSHOTS; SUBSTRATE BINDING; SUBSTRATE RECOGNITION;

POLYSACCHARIDES;

DISACCHARIDE; HEPARIN; HEPARIN LYASE; OLIGOSACCHARIDE;

ARTICLE; BACTEROIDES THETAIOTAOMICRON; CATALYSIS; CONTROLLED STUDY; CRYSTAL STRUCTURE; DEPOLYMERIZATION; ENZYME ACTIVE SITE; ENZYME KINETICS; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; MUTATIONAL ANALYSIS; NONHUMAN; PRIORITY JOURNAL; STRUCTURE ANALYSIS;

BACTEROIDES THETAIOTAOMICRON;

EID: 71749109423     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M109.025338     Document Type: Article

References (37)

1. Casu, B. (1985) Adv. Carbohydr. Chem. Biochem. 43, 51-134
2. Capila, I., and Linhardt, R. J. (2002) Angew. Chem. Int. Ed. 41, 390-412
3. Imberty, A., Lortat-Jacob, H., and Pérez, S. (2007) Carbohydr. Res. 342, 430-439
4. Ernst, S., Langer, R., Cooney, C. L., and Sasisekharan, R. (1995) Crit. Rev. Biochem. Mol. Biol. 30, 387-444
5. Gacesa, P. (1987) FEBS Lett. 212, 199-202
6. Linhardt, R. J., Avci, F. Y., Toida, T., Kim, Y. S., and Cygler, M. (2006) Adv. Pharmacol. 53, 187-215
7. Rigden, D. J., Littlejohn, J. E., Joshi, H. V., de Groot, B. L., and Jedrzejas, M. J. (2006) J. Mol. Biol. 358, 1165-1178
8. Yip, V. L., and Withers, S. G. (2006) Curr. Opin. Chem. Biol. 10, 147-155
9. Michel, G., Pojasek, K., Li, Y., Sulea, T., Linhardt, R. J., Raman, R., Prabhakar, V., Sasisekharan, R., and Cygler, M. (2004) J. Biol. Chem. 279, 32882-32896
10. Lohse, D. L., and Linhardt, R. J. (1992) J. Biol. Chem. 267, 24347-24355
11. Godavarti, R., and Sasisekharan, R. (1996) Biochem. Biophys. Res. Commun. 229, 770-777
12. Shaya, D., Tocilj, A., Li, Y., Myette, J., Venkataraman, G., Sasisekharan, R., and Cygler, M. (2006) J. Biol. Chem. 281, 15525-15535
13. Guerrini, M., Beccati, D., Shriver, Z., Naggi, A., Viswanathan, K., Bisio, A., Capila, I., Lansing, J. C., Guglieri, S., Fraser, B., Al-Hakim, A., Gunay, N. S., Zhang, Z., Robinson, L., Buhse, L., Nasr, M., Woodcock, J., Langer, R., Venkataraman, G., Linhardt, R. J., Casu, B., Torri, G., and Sasisekharan, R. (2008) Nat. Biotechnol. 26, 669-775
14. Otwinowski, Z., and Minor, W. (1997) Methods Enzymol. 276, 307-326
15. Rice, L. M., Earnest, T. N., and Brünger, A. T. (2000) Acta Crystallogr. Sect. D Biol. Crystallogr. 56, 1413-1420
16. Schneider, T. R., and Sheldrick, G. M. (2002) Acta Crystallogr. Sect. D Biol. Crystallogr. 58, 1772-1779
17. Bricogne, G., Vonrhein, C., Flensburg, C., Schiltz, M., and Paciorek, W. (2003) Acta Crystallogr. Sect. D Biol. Crystallogr. 59, 2023-2030
18. Emsley, P., and Cowtan, K. (2004) Acta Crystallogr. Sect. D Biol. Crystallogr. 60, 2126-2132
19. Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Acta Crystallogr. Sect. D Biol. Crystallogr. 53, 240-255
20. Terwilliger, T. C., and Berendzen, J. (1999) Acta Crystallogr. Sect. D Biol. Crystallogr. 55, 849-861
21. Terwilliger, T. C. (2001) Acta Crystallogr. Sect. D Biol. Crystallogr. 57, 1763-1775
22. 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
23. Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thronton, J. M. (1993) J. Appl. Crystallogr. 26, 283-291
24. Yang, V. C., Linhardt, R. J., Bernstein, H., Cooney, C. L., and Langer, R. (1985) J. Biol. Chem. 260, 1849-1857
25. Andreeva, A., Howorth, D., Brenner, S. E., Hubbard, T. J., Chothia, C., and Murzin, A. G. (2004) Nucleic Acids Res. 32, D226-D229
26. Davies, G. J., Wilson, K. S., and Henrissat, B. (1997) Biochem. J. 321, 557-559
27. Delano, W. L. (2004) The PyMOL Molecular Graphics System, DeLano Scientific LLC, San Carlos, CA
28. Money, V. A., Smith, N. L., Scaffidi, A., Stick, R. V., Gilbert, H. J., and Davies, G. J. (2006) Angew. Chem. Int. Ed. 45, 5136-5140
29. Kuroki, R., Weaver, L. H., and Matthews, B. W. (1993) Science 262, 2030-2033
30. Strynadka, N. C., and James, M. N. (1996) EXS 75, 185-222
31. Baker, N. A., Sept, D., Joseph, S., Holst, M. J., and McCammon, J. A. (2001) Proc. Natl. Acad. Sci. U.S.A. 98, 10037-10041
32. Ogura, K., Yamasaki, M., Mikami, B., Hashimoto, W., and Murata, K. (2008) J. Mol. Biol. 380, 373-385
33. Li, S., Kelly, S. J., Lamani, E., Ferraroni, M., and Jedrzejas, M. J. (2000) EMBO J. 19, 1228-1240
34. Gerlt, J. A., and Gassman, P. G. (1992) J. Am. Chem. Soc. 114, 5928-5934
35. Kato-Toma, Y., Iwashita, T., Masuda, K., Oyama, Y., and Ishiguro, M. (2003) Biochem. J. 371, 175-181
36. Cantarel, B. L., Coutinho, P. M., Rancurel, C., Bernard, T., Lombard, V., and Henrissat, B. (2009) Nucleic Acids Res. 37, D233-D238
37. Yamasaki, M., Ogura, K., Hashimoto, W., Mikami, B., and Murata, K. (2005) J. Mol. Biol. 352, 11-21