Molecular modeling of family GH16 glycoside hydrolases: Potential roles for xyloglucan transglucosylases/hydrolases in cell wall modification in the poaceae

Protein Science

Volumn 13, Issue 12, 2004, Pages 3200-3213

  Strohmeier, Marco ^a   Hrmova, Maria ^b   Fischer, Markus ^a   Harvey, Andrew J ^b   Fincher, Geoffrey B ^b   Pleiss, Jürgen ^a  

^a UNIVERSITY OF STUTTGART   (Germany)

^b UNIVERSITY OF ADELAIDE   (Australia)

Author keywords

galactanases, (1,3 1,3; 1,4) D glucan endohydrolases; (1,3; 1,4) D glucan endohydrolases; Database; Homology modeling; Xyloglucan transglucosylases

Indexed keywords

ARABINOXYLAN; BETA 1,3 GALACTANASE; BETA 1,4 GALACTANASE; GLUCAN; GLUCAN BETA 1,3:1,4 ENDOHYDROLASE; GLYCOSIDASE; PROTEIN GH16; UNCLASSIFIED DRUG; XYLOGLUCAN TRANSGLUCOSYLASE;

AMINO ACID SEQUENCE; ARTICLE; ASPEN; CATALYSIS; CELL WALL; DATA BASE; ENZYME ACTIVE SITE; ENZYME SPECIFICITY; ENZYME SUBSTRATE; GRASS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POACEAE; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN FUNCTION; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; UNINDEXED SEQUENCE;

AMINO ACID SEQUENCE; CELL WALL; ENDO-1,4-BETA XYLANASES; GLUCANS; GLYCOSIDE HYDROLASES; GLYCOSYLTRANSFERASES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYLOGENY; PLANT COMPONENTS; POACEAE; SEQUENCE HOMOLOGY; SEQUENCE HOMOLOGY, AMINO ACID; XYLANS;

EMBRYOPHYTA; POACEAE; POPULUS;

EID: 9344241402     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.04828404     Document Type: Article

References (63)

1. Anderson, M.A. and Stone, B.A. 1975. A new substrate for investigating the specificity of β-D-glucan hydrolases. FEBS Lett. 52: 202-207.
2. Bachman, E.S. and McClay, D.R. 1996. Molecular cloning of the first metazoan β-1,3 glucanase from eggs of the sea urchin Strongylocenlrotus purpuratus. Proc. Natl. Acad. Sci. 93: 6808-6813.
3. Barbeyron, T., Gerard, A., Potin, P., Henrissat, B., and Kloareg, B. 1998. The κ-carrageenase of the marine bacterium Cytophaga drobachiensis: Structural and phylogenetic relationships within family-16 glycoside hydrolases. Mol. Biol. Evol. 15: 528-537.
4. Benson, D.A., Boguski, M.S., Lipman, D.J., Ostell, J., Ouellette, B.F., Rapp, B.A., and Wheeler, D.L. 1999. GenBank. Nucleic Acids Res. 27: 12-17.
5. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. 2000. The Protein Data Bank. Nucleic Acids Res. 28: 235-242.
6. Carpita, N.C. and Gibeaut, D.M. 1993. Structural models of primary cell walls in flowering plants: Consistency of molecular structure with the physical properties of the walls during growth. Plant J. 3: 1-30.
7. Carpita, N.C., Defernez, M., Findlay, K., Wells, B., Shoue, D.A., Catchpole, G., Wilson, R.H., and McCann, M.C. 2001. Cell wall architecture of the elongating maize coleoptile. Plant Physiol. 127: 551-565.
8. Corpet, F., Gouzy, J., and Kahn, D. 1998. The ProDom database of protein domain families. Nucleic Acids Res. 26: 323-326.
9. Cosgrove, D.J. 1999. Enzymes and other agents that enhance cell wall extensibility. Annu. Rev. Plant Physiol. Plant Mol. Biol. 50: 391-417.
10. Coutinho, P.M. and Henrissat, B. 1999. Carbohydrate-active enzymes: An integrated database approach. In Recent advances in carbohydrate bioengineering (eds. H.J. Gilbert et al.), pp. 3-12. The Royal Society of Chemistry, Cambridge, UK.
11. Devereux, J., Haeberli, P., and Smithies, O. 1984. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 12: 387-395.
12. Engh, R. and Huber, R. 1991. Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallogr. A 47: 392-400.
13. Fanutti, C., Gidley, M.J., and Reid, J.S.G. 1993. Action of a pure xyloglucan endo-transglycosylase (formerly called xyloglucan-specific endo-(1-4)-β-D-glucanase) from the cotyledons of germinated nasturtium seeds. Plant J. 3: 691-700.
14. Farkas, V., Sulova, Z., Stratilova, E., Hanna, R., and Maclachlan, G. 1992. Cleavage of xyloglucan by nasturtium seed xyloglucanase and transglycosylation to xyloglucan subunit oligosaccharides. Arch. Biochem. Biophys. 298: 365-370.
15. Fincher, G.B. 1993. Cell wall metabolism in barley. In Barley: Genetics, biochemistry, molecular biology and biotechnology (ed. P.R. Shewry), pp. 413-437. CAB International Wallingford, Oxon, UK.
16. Fischer, M. and Pleiss, J. 2003. The Lipase Engineering Database: A navigation and analysis tool for protein families. Nucleic Acids Res. 31: 319-321.
17. Fry, S.C. 1989. Cellulases, hemicellulases and auxin-stimulated growth: A possible relationship. Physiol. Plant 72: 532-536.
18. Fry, S.C., Smith, R.C., Renwick, K.F., Martin, D.J., Hodge, S.K., and Matthews, K.J. 1992. Xyloglucan endotransglycosylase, a new wall-loosening enzyme activity from plants. Biochem. J. 282: 821-828.
19. Goff, S.A. 2002. Collaborating on the rice genome. Science 296: 45-46.
20. Gouzy, J., Corpet, F., and Kahn, D. 1996. Graphical interface for ProDom domain families. Trends Biochem. Sci. 21: 493.
21. Guex, N. and Peitsch, M.C. 1997. SWISS-MODEL and the Swiss-Pdb Viewer: An environment for comparative protein modeling. Electrophoresis 18: 2714-2723.
22. Hahn, M., Keitel, T., and Heinemann, U. 1995. Crystal and molecular structure at 0.16-nm resolution of the hybrid Bacillus endo-1,3-1,4-β-D- glucan 4-glucanohydrolase H(A16-M). Eur. J. Biochem. 232: 849-858.
23. Harvey, A.J., Hrmova, M., De Gori, R., Varghese, J.N., and Fincher, G.B. 2000. Comparative modeling of the three-dimensional structures of family 3 glycoside hydrolases. Proteins 41: 257-269.
24. Hayashi, T. 1989. Xyloglucans in the primary cell wall. Annu. Rev. Plant Physiol. Plant Mol. Biol. 40: 139-168.
25. Higgins, D.G., Thompson, J.D., and Gibson, T.J. 1996. Using CLUSTAL for multiple sequence alignments. Methods Enzymol. 266: 383-402.
26. Høj, P.B. and Fincher, G.B. 1995. Molecular evolution of plant β-D-glucan endohydrolases. Plant J. 7: 367-379.
27. Hrmova, M. and Fincher, G.B. 2001. Structure-function relationships of β-D-glucan endo- and exohydrolases from higher plants. Plant Mol. Biol. 47: 73-91.
28. Ishimaru, M. and Kobayashi, S. 2002. Expression of a xyloglucan endo-transglycosylase gene is closely related to grape berry softening. Plant Sci. 162: 621-628.
29. Jeanmougin, F., Thompson, J.D., Gouy, M., Higgins, D.G., and Gibson, T.J. 1998. Multiple sequence alignment with Clustal X. Trends Biochem. Sci. 23: 403-405.
30. Johansson, P., Brumer III, H., Baumann, M.J., Kallas, Å.M., Henriksson, H., Denman, S.E., Teeri, T.T., and Jones, A.T. 2004. Crystal structures of a poplar xyloglucan endotransglycosylase reveal details of transglycosylation acceptor binding. Plant Cell 16: 874-886.
31. Jones, T., Zou, J.-Y., Cowan, S., and Kjeldgaard, M. 1991. Improved methods for building protein models in electrone density maps and the location of errors in these models. Acta Crystallogr. A 47: 100-119.
32. Keitel, T., Simon, O., Borriss, R., and Heinemann, U. 1993. Molecular and active-site structure of a Bacillus 1,3-1,4-β-glucanase. Proc. Natl. Acad. Sci. 90: 5287-5291.
33. Kerr, E.M. and Fry, S.C. 2003. Pre-formed xyloglucans and xylans increase in molecular weight in three distinct compartments of a maize cell-suspension culture. Planta 217: 327-339.
34. Kloareg, B. and Quatrano, R.S. 1988. Structure of the cell walls of marine algae and ecophysical functions of the matrix polysaccharides. Oceanogr. Mar. Biol. Annu. Rev. 26: 259-315.
35. Knogge, W. 2002. A virulence determinants and elicitors. In The Mycota: Agricultural applications, Vol. XI (ed. F. Kempken), pp. 289-310. Springer Verlag, Berlin.
36. Krengel, U. and Dijkstra, B.W. 1996. Three-dimensional structure of endo-1,4-β-xylanase I from Aspergillus niger: Molecular basis for its low pH optimum. J. Mol. Biol. 263: 70-78.
37. Laskowski, R.A., MacArthur, M.W., Moss, D.S., and Thornton, J.M. 1993. PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26: 283-291.
38. Lemesle-Varloot, L., Henrissat, B., Gaboriaud, C., Bissery, V., Morgat, A., and Momon, J.P. 1990. Hydrophobic cluster analysis: Procedures to derive structural and functional information from 2-D-representation of protein sequences. Biochimie 72: 555-574.
39. Louw, M.E., Reid, S.J., and Watson, T.G. 1993. Characterization, cloning and sequencing of a thermostable endo-(1,3-1,4)-β-glucanase-encoding gene from an alkalophilic Bacillus brevis. Appl. Microbiol. Biotechnol. 38: 507-513.
40. Mengden, K., Hahn, M., and Deisig, H. 1996. Morphogenesis and mechanisms of penetration by plant pathogenic fungi. Annu. Rev. Phytopatol. 34: 367-386.
41. Michel, G., Chantalat, L., Duee, E., Barbeyron, T., Henrissat, B., Kloareg, B., and Dideberg, O. 2001. The κ-carrageenase of P. carrageenovora features a tunnel-shaped active site: A novel insight in the evolution of Clan-B glycoside hydrolases. Structure 9: 513-525.
42. Nishitani, K. 1997. The role of endoxyloglucan transferase in the organization of plant cell wall. Int. Rev. Cytol. 173: 157-206.
43. Okazawa, K., Sato, Y., Nakagawa, T., Asada, K., Kato, I., Tomita, E., and Nishitani, K. 1993. Molecular cloning and cDNA sequencing of endoxyloglucan transferase, a novel class of glycosyltransferase that mediates molecular grafting between matrix polysaccharides in plant cell walls. J. Biol. Chem. 268: 25364-25368.
44. Page, R.D.M. 1996. TREEVIEW: An application to display phylogenetic trees on personal computers. Comp. Appl. Biosci. 12: 357-358.
45. Parrish, F.W., Perlin, A.S., and Reese, E.T. 1960. Selective enzymolysis of poly-β-D-glucans, and the structure of the polymers. Can. J. Chem 38: 2094-2104.
46. Pennel, R. 1998. Cell walls: Structures and signals. Curr. Opin. Plant Biol. 1: 504-510.
47. Ramachandran, G.N., Ramakrishnan, C., and Sasisekharan, V. 1963. Stereochemistry of polypeptide chain configurations. J. Mol. Biol. 7: 95-99.
48. Rose, J.K.C., Braam, J., Fry, S.C., and Nishitani, K. 2002. The XTH family of enzymes involved in xyloglucan endotransglucosylation and endohydrolysis: Current perspectives and a new unifying nomenclature. Plant Cell Physiol. 43: 1421-1435.
49. Sali, A. and Blundell, T.L. 1993. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234: 779-815.
50. Sakurai, N. and Masuda, Y. 1978. Auxin-induced changes in barley coleoptile cell wall composition. Plant Cell Physiol. 19: 1217-1223.
51. Schimming, S., Schwarz, W.H., and Staudenbauer, W.L. 1992. Structure of the Clostridium thermocellum gene licB and the encoded β-1,3-1,4-glucanase: A catalytic region homologous to Bacillus lichenase joined to the reiterated domain of clostridial cellulases. Eur. J. Biochem. 204: 13-19.
52. Schmidt, H.A., Strimmer, K., Vingron, M., and von Haeseler, A. 2002. TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18: 502-504.
53. Schünmann, P.H.D., Smith, R.C., Lang, V., Matthew, R., and Chandler, P.M. 1997. Expression of XET-related genes and its relation to elongation in leaves of barley (Hordeum vulgare L.). Plant Cell Env. 20: 1439-1450.
54. Shibuya, N. and Misaki, A. 1978. Structure of hemicellulose isolated from rice endosperm cell wall: Mode of linkages and sequences in xyloglucan, β-D-glucan and arabinoxylan. Agric. Biol. Chem. 42: 2267-2274.
55. Shibuya, N., Misaki, A., and Iwasaki, T. 1983. The structure of arabinoxylan and arabinoglucuronoxylan isolated from rice endosperm cell walls. Agric. Biol. Chem. 47: 2223-2230.
56. Smith, R.C. and Fry, S.C. 1991. Endotransglycosylation of xyloglucans in plant cell suspension cultures. Biochem. J. 279: 529-535.
57. Smith, R.C., Matthews, P.R., Schünmann, P.H.D., and Chandler, P.M. 1997. The regulation of leaf elongation and xyloglucan endotransglycosylase by gibberellin in Himalaya barley (Hordeum vulgare L.) J. Exp. Bot. 47: 1395-1404.
58. Smith, T.F. and Waterman, M.S. 1981. Identification of common molecular subsequences. J. Mol. Biol. 147: 195-197.
59. Tahir, T.A., Berrin, J.G., Flatman, R., Roussel, A., Roepstorff, P., Williamson, G., and Juge, N. 2002. Specific characterization of substrate and inhibitor binding sites of a glycosyl hydrolase family 11 xylanase from Aspergillus niger. J. Biol. Chem. 277: 44035-44043.
60. 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.
61. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., and Higgins, D.G. 1997. The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25: 4876-4882.
62. Wu, Y., Spollen, W.G., Sharp, R.E., Hetherington, P.R., and Fry, S.C. 1994. Root growth maintenance at low water potentials (increased activity of xyloglucan endotransglycosylase and its possible regulation by abscisic acid). Plant Physiol. 106: 607-615.
63. Yahata, N., Watanabe, T., Nakamura, Y., Yamamoto, Y., Kainimiya, S., and Tanaka, H. 1990. Structure of the gene encoding β-1,3-glucanase A1 of Bacillus circulans WL-12. Gene 86: 113-117.