Identification of the substrate interaction region of the chitin-binding domain of Streptomyces griseus chitinase C

Journal of Biochemistry

Volumn 139, Issue 3, 2006, Pages 483-493

  Akagi, Ken Ichi ^a   Watanabe, Jun ^b   Hara, Masashi ^b   Kezuka, Yuichiro ^c   Chikaishi, Eriko ^a   Yamaguchi, Tohru ^d   Akutsu, Hideo ^a   Nonaka, Takamasa ^c   Watanabe, Takeshi ^b   Ikegami, Takahisa ^a  

^a OSAKA UNIVERSITY   (Japan)

^b NIIGATA UNIVERSITY   (Japan)

^c NAGAOKA UNIVERSITY OF TECHNOLOGY   (Japan)

^d SHIONOGI AND CO LTD   (Japan)

Author keywords

Cellulose; Cellulose binding domain; Chitin binding domain; Chitinase

Indexed keywords

CARBOHYDRATE BINDING PROTEIN; CELLULOSE; CHITIN; CHITINASE; CHITINASE C; GLUCAN SYNTHASE; POLYSACCHARIDE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BACILLUS CIRCULANS; BETA SHEET; BINDING SITE; CARBON NUCLEAR MAGNETIC RESONANCE; CONTROLLED STUDY; ENZYME ANALYSIS; ENZYME BINDING; ENZYME CONFORMATION; ENZYME STRUCTURE; ENZYME SUBSTRATE; NITROGEN NUCLEAR MAGNETIC RESONANCE; NONHUMAN; PECTOBACTERIUM CHRYSANTHEMI; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTON NUCLEAR MAGNETIC RESONANCE; SPECIES DIFFERENCE; STREPTOMYCES GRISEUS;

AMINO ACID SEQUENCE; BINDING SITES; CELLULOSE; CHITIN; CHITINASE; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, TERTIARY; STREPTOMYCES GRISEUS; SUBSTRATE SPECIFICITY;

BACILLUS CIRCULANS; BACTERIA (MICROORGANISMS); EMBRYOPHYTA; ERWINIA CHRYSANTHEMI; STREPTOMYCES GRISEUS;

EID: 33646352731     PISSN: 0021924X     EISSN: None     Source Type: Journal    
DOI: 10.1093/jb/mvj062     Document Type: Article

References (47)

1. Kurita, K. (2001) Controlled functionalization of the polysaccharide chitin. Prog. Polym. Sci. 26, 1921-1971
2. Henrissat, B. (1991) A classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem. J. 280, 309-316
3. Henrissat, B. and Bairoch, A. (1993) New families in the classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem. J. 293, 781-788
4. Perrakis, A., Tews, I., Dauter, Z., Oppenheim, A.B., Chet, I., Wilson, K.S., and Vorgias, C.E. (1994) Crystal structure of a bacterial chitinase at 2.3 Å resolution. Structure 2, 1169-1180
5. Davies, G. and Henrissat, B. (1995) Structure and mechanism of glycosyl hydrolases. Structure 3, 853-859
6. Tews, I., Terwissha van Scheltinga, A.C., Perrakis, A., Wilson, K.S., and Dijkatra, B.W. (1997) Substrate-assisted catalysis unifies two families of chitinolytic enzymes. J. Am. Chem. Soc. 119, 7954-7959
7. Brameld, K.A., Shrader, W.D., Imperiali, B., and Goddard, W.A. 3rd. (1998) Substrate assistance in the mechanism of family 18 chitinases: theoretical studies of potential intermediates and inhibitors. J. Mol. Biol. 280, 913-923
8. Hart, P.J., Pfluger, H.D., Monzingo, A.F., Hollis, T., and Robertus, J.D. (1995) The refined crystal structure of an endochitinase from Hordeum vulgare L. seeds at 1.8 Å resolution. J. Mol. Biol. 248, 402-413
9. Garcia-Casado, G., Collada, C., Allona, I., Casado, R., Pacios, L.F., Aragoncillo, C., and Gomez, L. (1998) Site-directed mutagenesis of active site residues in a class I endochitinase from chestnut seeds. Glycobiology 8, 1021-1028
10. Ohno, T., Armand, S., Hata, T., Nikaidou, N., Henrissat, B., Mitsutomi, M., and Watanabe, T. (1996) A modular family 19 chitinase found in the prokaryotic organism Streptomyces griseus HUT 6037. J. Bacteriol. 178, 5065-5070
11. Watanabe, T., Kanai, R., Kawase, T., Tanabe, T., Mitsutomi, M., Sakuda, S., and Miyashita K. (1999) Family 19 chitinases of Streptomyces species: characterization and distribution. Microbiology 145, 3353-3363
12. Itoh, Y., Takahashi, K., Takizawa, H., Nikaidou, N., Tanaka, H., Nishihashi, H., Watanabe, T., and Nishizawa, Y. (2003) Family 19 chitinase of Streptomyces griseus HUT6037 increases plant resistance to the fungal disease. Biosci. Biotechnol. Biochem. 67, 847-855
13. Tomme, P., Warren, R.A., Miller, R.C., Kilburn, D.G. Jr., and Gilkes, N.R. (1995) Cellulose-binding domains: classification and properties in Enzymatic Degradation of Insoluble Polysaccharides (Saddler, J.N. and Penner, M., eds.) pp. 142-163, American Chemical Society, Washington
14. Collinge, D.B., Kragh, K.M., Mikkelsen, J.D., Nielsen, K.K., Rasmussen, U., and Vad, K. (1993) Plant chitinases. Plant J. 3, 31-40
15. Wright, C.S. (1987) Refinement of the crystal structure of wheat germ agglutinin isolectin 2 at 1.8 Å resolution. J. Mol. Biol. 194, 501-529
16. Hashimoto, M., Ikegami, T., Seino, S., Ohuchi, N., Fukada, H., Sugiyama, J., Shirakawa, M., and Watanabe, T. (2000) Expression and characterization of the chitin-binding domain of chitinase A1 from Bacillus circulans WL-12. J. Bacteriol. 182, 3045-3054
17. Jee, J.G., Ikegami, T., Hashimoto, M., Kawabata, T., Ikeguchi, M., Watanabe, T., and Shirakawa, M. (2002) Solution structure of the fibronectin type III domain from Bacillus circulans WL-12 chitinase A1. J. Biol. Chem. 277, 1388-1397
18. Brun, E., Moriaud, F., Gans, P., Blackledge, M.J., Barras, F., and Marion, D. (1997) Solution structure of the cellulose-binding domain of the endoglucanase Z secreted by Erwinia chrysanthemi. Biochemistry 36, 16074-16086
19. Itoh, Y., Kawase, T., Nikaidou, N., Fukada, H., Mitsutomi, M., Watanabe, T., and Itoh, Y. (2002) Functional analysis of the chitin-binding domain of a family 19 chitinase from Streptomyces griseus HUT6037: substrate-binding affinity and cis-dominant increase of antifungal function. Biosci. Biotechnol. Biochem. 66, 1084-1092
20. Ikegami, T., Okada, T., Hashimoto, M., Seino, S., Watanabe, T., and Shirakawa, M. (2000) Solution structure of the chitin-binding domain of Bacillus circulans WL-12 chitinase A1. J. Biol. Chem. 275, 13654-13661
21. Cavanagh, J., Fairbrother, W.J., Palmer, A.G. III, and Skelton, N.J. (1996) Protein NMR Spectroscopy, Academic Press, San Diego
22. 13C-labeled proteins via scalar couplings. J. Am. Chem. Soc. 115, 11054-11055
23. Delaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer, J., and Bax, A. (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277-293
24. Goddard, T.D. and Kneller, D.G. SPARKY 3, University of California, San Francisco
25. NCγ couplings. J. Am. Chem. Soc. 119, 1803-1804
26. Wüthrich, K. (1986) NMR of Proteins and Nucleic Acids, John Wiley & Sons, New York
27. Güntert, P., Mumenthaler, C., and Wüthrich, K. (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol. 273, 283-298
28. 13C labeling. Biochemistry 28, 7510-7516
29. Cornilescu, G., Delaglio, F., and Bax, A. (1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J. Biomol. NMR 13, 289-302
30. Laskowski, R.A., Rullmannn, J.A., MacArthur, M.W., Kaptein, R., and Thornton, J.M. (1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 8, 477-486
31. 15N NMR relaxation. Biochemistry 33, 5984-6003
32. Lipari, G. and Szabo, A. (1982) Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. J. Am. Chem. Soc. 104, 4546-4570
33. Dosset, P., Hus, J.C., Blackledge, M., and Marion, D. (2000) Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data. J. Biomol. NMR 16, 23-28
34. 13C NMR chemical shifts can predict disulfide bond formation. J. Biomol. NMR 18, 165-171
35. Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.G., and Ferrin, T.E. (2004) UCSF Chimera - A visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605-1612
36. van Aalten, D.M., Synstad, B., Brurberg, M.B., Hough, E., Ruse, B.W., Eijsink, V.G., and Wierenga, R.K. (2000) Structure of a two-domain chitotriosidase from Serratia marcescens at 1.9-Å resolution. Proc. Natl. Acad. Sci. USA 97, 5842-5847
37. Eisenmesser, E.Z., Millet, O., Labeikovsky, W., Korzhnev, D.M., Wolf-Watz, M., Bosco, D.A., Skalicky, J.J., Kay, L.E., and Kern, D. (2005) Intrinsic dynamics of an enzyme underlies catalysis. Nature 438, 117-121
38. Simpson, H.D. and Barras, F. (1999) Functional analysis of the carbohydrate-binding domains of Erwinia chrysanthemi Cel5 (Endoglucanase Z) and an Escherichia coli putative chitinase. J. Bacteriol. 181, 4611-4616
39. Tormo, J., Lamed, R., Chirino, A.J., Morag, E., Bayer, E.A., Shoham, Y., and Steitz, T.A. (1996) Crystal structure of a bacterial family-III cellulose-binding domain: a general mechanism for attachment to cellulose. EMBO J. 15, 5739-5751
40. Xu, G.Y., Ong, E., Gilkes, N.R., Kilburn, D.G., Muhandiram, D.H., Harris-Brandts, M., Carver, J.P., Kay, L.E., and Harvey, T.S. (1995) Solution structure of a cellulose-binding domain from Cellulomonas fimi by nuclear magnetic resonance spectroscopy. Biochemistry 34, 6993-7009
41. Kraulis, J., Clore, G.M., Nilges, M., Jones, T.A., Pettersson, G., Knowles, J., and Gronenborn, A.M. (1989) Determination of the three-dimensional solution structure of the C-terminal domain of cellobiohydrolase I from Trichoderma reesei. A study using nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing. Biochemistry 28, 7241-7257
42. Mattinen, M.L., Kontteli, M., Kerovuo, J., Linder, M., Annila, A., Lindeberg, G., Reinikainen, T., and Drakenberg, T. (1997) Three-dimensional structures of three engineered cellulose-binding domains of cellobiohydrolase I from Trichoderma reesei. Protein Sci. 6, 294-303
43. Ferrandon, S., Sterzenbach, T., Mersha, F.B., and Xu, M.Q. (2003) A single surface tryptophan in the chitin-binding domain from Bacillus circulans chitinase A1 plays a pivotal role in binding chitin and can be modified to create an elutable affinity tag. Biochim. Biophys. Acta 1621, 31-40
44. ChiA1 from chitinase A1 of Bacillus circulans alters substrate specificity: use of a green fluorescent protein binding assay. Arch. Biochem. Biophys. 426, 286-297
45. Thompson, J.D., Higgins, D.G., and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680
46. Holm, L. and Sander, C. (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123-138
47. Koradi, R., Billeter, M., and Wuthrich, K. (1996) MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14, 51-55