Characterization of glycosynthase mutants derived from glycoside hydrolase family 10 xylanases

Bioscience, Biotechnology and Biochemistry

Volumn 70, Issue 5, 2006, Pages 1210-1217

  Sugimura, Masahiro ^a   Nishimoto, Mamoru ^a   Kitaoka, Motomitsu ^a  

^a NATIONAL FOOD RESEARCH INSTITUTE   (Japan)

Author keywords

xylobiosyl fluoride; Glycoside hydrolase family 10; Glycosynthase; Subsite structure; Xylanase

Indexed keywords

BACTERIA; BIOCHEMISTRY; ENZYME KINETICS; FLUORINE COMPOUNDS; MOLECULAR STRUCTURE;

Α-XYLOBIOSYL FLUORIDE; GLYCOSIDE HYDROLASE FAMILY 10; GLYCOSYNTHASE; XYLANASE;

ENZYMES;

DRUG DERIVATIVE; GLYCOSIDASE; XYLAN 1,4 BETA XYLOSIDASE; XYLOPYRANOSE; XYLOSE;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; BACILLUS; BIOSYNTHESIS; CELLULOMONAS; CHEMISTRY; CLOSTRIDIUM; ENZYME SPECIFICITY; ENZYMOLOGY; GENETICS; MOLECULAR GENETICS; MUTATION; THERMOTOGA MARITIMA;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; BACILLUS; CELLULOMONAS; CLOSTRIDIUM; GLYCOSIDE HYDROLASES; MOLECULAR SEQUENCE DATA; MUTATION; SUBSTRATE SPECIFICITY; THERMOTOGA MARITIMA; XYLOSE; XYLOSIDASES;

BACILLUS HALODURANS; CELLULOMONAS; CELLULOMONAS FIMI; CLOSTRIDIUM; CLOSTRIDIUM STERCORARIUM; THERMOTOGA MARITIMA;

EID: 33646809040     PISSN: 09168451     EISSN: 13476947     Source Type: Journal    
DOI: 10.1271/bbb.70.1210     Document Type: Article

References (47)

1. Biely, P., Microbial xylanolytic systems. Trends Biotechnol., 3, 286-290 (1985).
2. Collins, T., Gerday, C., and Feller, G., Xylanases, xylanase families and extremophilic xylanases. FEMS Microbiol. Rev., 29, 3-23 (2005).
3. Henrissat, B., A classification of glycosyl hydrolases based on amino-acid sequence similarities. Biochem. J., 280, 309-316 (1991).
4. Henrissat, B., and Davies, G., Structural and sequence-based classification of glycoside hydrolases. Curr. Opin. Struct. Biol., 7, 637-644 (1997).
5. McCarter, J. D., and Withers, S. G., Mechanisms of enzymatic glycoside hydrolysis. Curr. Opin. Struct. Biol., 4, 885-892 (1994).
6. White, A., and Rose, D. R., Mechanism of catalysis by retaining β-glycosyl hydrolases. Curr. Opin. Struct. Biol., 7, 645-651 (1997).
7. Derewenda, U., Swenson, L., Green, R., Wei, Y., Morosoli, R., Shareck, F., Kluepfel, D., and Derewenda, Z. S., Crystal structure, at 2.6-Å resolution, of the Streptomyces lividans xylanase A, a member of the F family of β-1,4-D-glycanases. J. Biol. Chem., 269, 20811-20814 (1994).
8. Dominguez, R., Souchon, H., Spinelli, S., Dauter, Z., Wilson, K. S., Chauvaux, S., Beguin, P., and Alzari, P. M., A common protein fold and similar active site in two distinct families of β-glycanases. Nat. Struct. Biol., 2, 569-576 (1995).
9. Fujimoto, Z., Kuno, A., Kaneko, S., Yoshida, S., Kobayashi, H., Kusakabe, I., and Mizuno, H., Crystal structure of Streptomyces olivaceoviridis E-86 β-xylanase containing xylan-binding domain. J. Mol. Biol., 300, 575-585 (2000).
10. Harris, G. W., Jenkins, J. A., Connerton, I., Cummings, N., Lo Leggio, L., Scott, M., Hazlewood, G. P., Laurie, J. I., Gilbert, H. J., and Pickersgill, R. W., Structure of the catalytic core of the family F xylanase from Pseudomonas fluorescens and identification of the xylopentaose-binding sites. Structure, 2, 1107-1116 (1994).
11. Natesh, R., Bhanumoorthy, P., Vithayathil, P. J., Sekar, K., Ramakumar, S., and Viswamitra, M. A., Crystal structure at 1.8Å resolution and proposed amino acid sequence of a thermostable xylanase from Thermoascus aurantiacus. J. Mol. Biol., 288, 999-1012 (1999).
12. Payan, F., Leone, P., Porciero, S., Furniss, C., Tahir, T., Williamson, G., Durand, A., Manzanares, P., Gilbert, H. J., Juge, N., and Roussel, A., The dual nature of the wheat xylanase protein inhibitor XIP-I: structural basis for the inhibition of family 10 and family 11 xylanases. J. Biol. Chem., 279, 36029-36037 (2004).
13. Pell, G., Szabo, L., Charnock, S. J., Xie, H., Gloster, T. M., Davies, G. J., and Gilbert, H. J., Structural and biochemical analysis of Cellvibrio japonicus xylanase 10C: how variation in substrate-binding cleft influences the catalytic profile of family GH-10 xylanases. J. Biol. Chem., 279, 11777-11788 (2004).
14. Pell, G., Taylor, E. J., Gloster, T. M., Turkenburg, J. P., Fontes, C. M., Ferreira, L. M., Nagy, T., Clark, S. J., Davies, G. J., and Gilbert, H. J., The mechanisms by which family 10 glycoside hydrolases bind decorated substrates. J. Biol. Chem., 279, 9597-9605 (2004).
15. Schmidt, A., Gubitz, G. M., and Kratky, C., Xylan binding subsite mapping in the xylanase from Penicillium simplicissimum using xylooligosaccharides as cryoprotectant. Biochemistry, 38, 2403-2412 (1999).
16. Teplitsky, A., Mechaly, A., Stojanoff, V., Sainz, G., Golan, G., Feinberg, H., Gilboa, R., Reiland, V., Zolotnitsky, G., Shallom, D., Thompson, A., Shoham, Y., and Shoham, G., Structure determination of the extracellular xylanase from Geobacillus stearothermophilus by selenomethionyl MAD phasing. Acta Crystallogr. D Biol. Crystallogr., 60, 836-848 (2004).
17. White, A., Withers, S. G., Gilkes, N. R., and Rose, D. R., Crystal structure of the catalytic domain of the β-1,4-glycanase cex from Cellulomonas fimi. Biochemistry, 33, 12546-12552 (1994).
18. Jenkins, J., Lo Leggio, L., Harris, G., and Pickersgill, R., β-Glucosidase, β-galactosidase, family A cellulases, family F xylanases and two barley glycanases form a superfamily of enzymes with 8-fold β/α architecture and with two conserved glutamates near the carboxy-terminal ends of β-strands four and seven. FEBS Lett., 362, 281-285 (1995).
19. Charnock, S. J., Spurway, T. D., Xie, H., Beylot, M. H., Virden, R., Warren, R. A., Hazlewood, G. P., and Gilbert, H. J., The topology of the substrate binding clefts of glycosyl hydrolase family 10 xylanases are not conserved. J. Biol. Chem., 273, 32187-32199 (1998).
20. Mackenzie, L. F., Wang, Q., Warren, R. A. J., and Withers, S. G., Glycosynthases: mutant glycosidases for oligosaccharide synthesis. J. Am. Chem. Soc., 120, 5583-5584 (1998).
21. Mayer, C., Jakeman, D. L., Mah, M., Karjala, G., Gal, L., Warren, R. A., and Withers, S. G., Directed evolution of new glycosynthases from Agrobacterium β-glucosidase: a general screen to detect enzymes for oligosaccharide synthesis. Chem. Biol., 8, 437-443 (2001).
22. Mayer, C., Zechel, D. L., Reid, S. P., Warren, R. A., and Withers, S. G., The E358S mutant of Agrobacterium sp. β-glucosidase is a greatly improved glycosynthase. FEBS Lett., 466, 40-44 (2000).
23. Nashiru, O., Zechel, D. L., Stoll, D., Mohammadzadeh, T., Warren, R. A. J., and Withers, S. G., β-Mannosynthase: synthesis of β-mannosides with a mutant β-mannosidase. Angew. Chem. Int. Ed. Engl., 40, 417-420 (2001).
24. Zechel, D. L., Reid, S. P., Stoll, D., Nashiru, O., Warren, R. A., and Withers, S. G., Mechanism, mutagenesis, and chemical rescue of a β-mannosidase from Cellulomonas fimi. Biochemistry, 42, 7195-7204 (2003).
25. Kim, Y. W., Lee, S. S., Warren, R. A., and Withers, S. G., Directed evolution of a glycosynthase from Agrobacterium sp. increases its catalytic activity dramatically and expands its substrate repertoire. J. Biol. Chem., 279, 42787-42793 (2004).
26. Trincone, A., Perugino, G., Rossi, M., and Moracci, M., A novel thermophilic glycosynthase that effects branching glycosylation. Bioorg. Med. Chem. Lett., 10, 365-368 (2000).
27. Lin, H., Tao, H., and Cornish, V. W., Directed evolution of a glycosynthase via chemical complementation. J. Am. Chem. Soc., 126, 15051-15059 (2004).
28. Hrmova, M., Imai, T., Rutten, S. J., Fairweather, J. K., Pelosi, L., Bulone, V., Driguez, H., and Fincher, G. B., Mutated barley (1,3)-β-D- glucan endohydrolases synthesize crystalline (1,3)-β-D-glucans. J. Biol. Chem., 277, 30102-30111 (2002).
29. Malet, C., and Planas, A., From β-glucanase to β- glucansynthase: glycosyl transfer to α-glycosyl fluorides catalyzed by a mutant endoglucanase lacking its catalytic nucleophile. FEBS Lett., 440, 208-212 (1998).
30. Faijes, M., Perez, X., Perez, O., and Planas, A., Glycosynthase activity of Bacillus licheniformis 1,3-1,4-β-glucanase mutants: specificity, kinetics, and mechanism. Biochemistry, 42, 13304-13318 (2003).
31. Ducros, V. M., Tarling, C. A., Zechel, D. L., Brzozowski, A. M., Frandsen, T. P., von Ossowski, I., Schulein, M., Withers, S. G., and Davies, G. J., Anatomy of glycosynthesis: structure and kinetics of the Humicola insolens Cel7B E197A and E197S glycosynthase mutants. Chem. Biol., 10, 619-628 (2003).
32. Boyer, V., Fort, S., Frandsen, T. P., Schulein, M., Cottaz, S., and Driguez, H., Chemoenzymatic synthesis of a bifunctionalized cellohexaoside as a specific substrate for the sensitive assay of cellulase by fluorescence quenching. Chemistry, 8, 1389-1394 (2002).
33. Fort, S., Boyer, V., Greffe, L., Davies, G. J., Moroz, O., Christiansen, L., Schulein, M., Cottaz, S., and Driguez, H., Highly efficient synthesis of β(1,4)-oligo- and -polysaccharides using a mutant cellulase. J. Am. Chem. Soc., 122, 5429-5437 (2000).
34. Okuyama, M., Mori, H., Watanabe, K., Kimura, A., and Chiba, S., α-Glucosidase mutant catalyzes "α-glycosynthase"-type reaction. Biosci. Biotechnol. Biochem., 66, 928-933 (2002).
35. Honda, Y., and Kitaoka, M., The first glycosynthase derived from an inverting glycoside hydrolase. J. Biol. Chem., 281, 1426-1431 (2006).
36. Zhengqiang, J., Kobayashi, A., Ahsan, M. M., Lite, L., Kitaoka, M., and Hayashi, K., Characterization of a thermostable family 10 endo-xylanase (xynB) from Thermotoga maritima that cleaves p-nitrophenyl-β-D-xyloside. J. Biosci. Bioeng., 92, 423-428 (2001).
37. Fukumura, M., Sakka, K., Shimada, K., and Ohmiya, K., Nucleotide sequence of the Clostridium stercorarium xynB gene encoding an extremely thermostable xylanase, and characterization of the translated product. Biosci. Biotechnol. Biochem., 59, 40-46 (1995).
38. Nishimoto, M., Honda, Y., Kitaoka, M., and Hayashi, K., A kinetic study on pH-activity relationship of XynA from alkaliphilic Bacillus halodurans C125 using aryl-xylobiosides. J. Biosci. Bioeng., 93, 428-430 (2002).
39. Gilkes, N. R., Warren, R. A., Miller, R. C., Jr., and Kilburn, D. G., Precise excision of the cellulose binding domains from two Cellulomonas fimi cellulases by a homologous protease and the effect on catalysis. J. Biol. Chem., 263, 10401-10407 (1988).
40. Hayashi, M., Hashimoto, M., and Noyori, R., Simple synthesis of glycosyl fluorides. Chem. Lett., 1747-1750 (1984).
41. Yokoyama, M., Methods of synthesis of glycosyl fluorides. Carbohydr. Res., 327, 5-14 (2000).
42. Nishimoto, M., Fushinobu, S., Miyanaga, A., Wakagi, T., Shoun, H., Sakka, K., Ohmiya, K., Nirasawa, S., Kitaoka, M., and Hayashi, K., Crystallization and preliminary X-ray analysis of xylanase B from Clostridium stercorarium. Acta Crystallogr. D Biol. Crystallogr., 60, 342-343 (2004).
43. Honda, Y., Kitaoka, M., Sakka, K., Ohmiya, K., and Hayashi, K., An investigation of the pH-activity relationship of Cex, a family 10 xylanase from Cellulomonas fimi: xylan inhibition and the influence of nitro-substituted aryl-β-D-xylobiosides on xylanase activity. J. Biosci. Bioeng., 93, 313-317 (2002).
44. Laemmli, U. K., Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature, 224, 680-685 (1970).
45. Kaneko, S., Ichinose, H., Fujimoto, Z., Kuno, A., Yura, K., Go, M., Mizuno, H., Kusakabe, I., and Kobayashi, H., Structure and function of a family 10 β-xylanase chimera of Streptomyces olivaceoviridis E-86 FXYN and Cellulomonas fimi Cex. J. Biol. Chem., 279, 26619-26626 (2004).
46. Kitaoka, M., Haga, K., Kashiwagi, Y., Sasaki, T., Taniguchi, H., and Kusakabe, I., Kinetic studies on p-nitrophenyl-cellobioside hydrolyzing xylanase from Cellvibrio gilvus. Biosci. Biotechnol. Biochem., 57, 1987-1989 (1993).
47. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., and Higgins, D. G., The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl. Acids Res., 25, 4876-4882 (1997).