Structural dissection of the reaction mechanism of cellobiose phosphorylase

Biochemical Journal

Volumn 398, Issue 1, 2006, Pages 37-43

  Hidaka, Masafumi ^a,b   Kitaoka, Motomitsu ^b   Hayashi, Kiyoshi ^b   Wakagi, Takayoshi ^a   Shoun, Hirofumi ^a   Fushinobu, Shinya ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b NATIONAL FOOD RESEARCH INSTITUTE   (Japan)

Author keywords

Carbohydrate active enzyme; Cellobiose phosphorylase; Chitobiose phosphorylase; Glycoside hydrolase family 94; Substrate specificity; X ray crystallography

Indexed keywords

COMPLEXATION; CONFORMATIONS; CRYSTAL STRUCTURE; ENZYME KINETICS; REACTION KINETICS; X RAY CRYSTALLOGRAPHY;

CARBOHYDRATE-ACTIVE ENZYME; CELLOBIOSE PHOSPHORYLASE; CHITOBIOSE PHOSPHORYLASE; GLYCOSIDE HYDROLASE FAMILY 94; SUBSTRATE SPECIFICITY;

ENZYMES;

CELLOBIOSE PHOSPHORYLASE ENZYME; CHITOBIOSE PHOSPHORYLASE ENZYME; GLUCOSE; GLUCOSE PHOSPHATE; GLUCOSE SULFATE; GLYCOSIDASE; N ACETYLGALACTOSAMINE; PHOSPHATE; PHOSPHORYLASE; SUGAR; SULFATE; UNCLASSIFIED DRUG;

ARTICLE; CARBOHYDRATE SYNTHESIS; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; ENZYME ACTIVE SITE; ENZYME ANALYSIS; ENZYME ENGINEERING; ENZYME KINETICS; ENZYME MECHANISM; ENZYME SPECIFICITY; ENZYME STRUCTURE; ENZYME SUBSTRATE; ENZYME SUBSTRATE COMPLEX; HYDROGEN BOND; PRIORITY JOURNAL; THREE DIMENSIONAL IMAGING;

BINDING SITES; CARBOHYDRATES; CELLVIBRIO; CRYSTALLOGRAPHY, X-RAY; GLUCOSYLTRANSFERASES; KINETICS; MODELS, MOLECULAR; PHOSPHATES; PROTEIN STRUCTURE, SECONDARY; SUBSTRATE SPECIFICITY; SULFATES;

CELLVIBRIO GILVUS;

EID: 33747201719     PISSN: 02646021     EISSN: None     Source Type: Journal    
DOI: 10.1042/BJ20060274     Document Type: Article

References (42)

1. Coutinho, P. and Henrissat, B. (1999) Carbohydrate-active enzymes: an integrated database approach. In Recent Advances in Carbohydrate Bioengineering (Gilbert, H. J., Davies, G. J., Henrissat, B. and Svensson, B., eds.), pp. 3-12, Royal Society of Chemistry, Cambridge
2. Geremia, S., Campagnolo, M., Schinzel, R. and Johnson, L. N. (2002) Enzymatic catalysis in crystals of Escherichia coli maltodextrin phosphorylase. J. Mol. Biol. 322, 413-423
3. O'Reilly, M., Watson, K. A. and Johnson, L. N. (1999) The crystal structure of the Escherichia coli maltodextrin phosphorylase-acarbose complex. Biochemistry 38, 5337-5345
4. O'Reilly, M., Watson, K. A., Schinzel, R., Palm, D. and Johnson, L. N. (1997) Oligosaccharide substrate binding in Escherichia coli maltodextrin phosphorylase. Nat. Struct. Biol. 4, 405-412
5. Watson, K. A., McCleverty, C., Geremia, S., Cottaz, S., Driguez, H. and Johnson, L. N. (1999) Phosphorylase recognition and phosphorolysis of its oligosaccharide substrate: answers to a long outstanding question. EMBO J. 18, 4619-4632
6. Gibson, R. P., Tarling, C. A., Roberts, S., Withers, S. G. and Davies, G. J. (2004) The donor subsite of trehalose-6-phosphate synthase-binary complexes with UDP-glucose and UDP-2-deoxy-2-fluoro-glucose at 2 Å resolution. J. Biol. Chem. 279, 1950-1955
7. Buschiazzo, A., Ugalde, J. E., Guerin, M. E., Shepard, W., Ugalde, R. A. and Alzari, P. M. (2004) Crystal structure of glycogen synthase: homologous enzymes catalyze glycogen synthesis and degradation. EMBO J. 23, 3196-3205
8. 6 barrel fold. Structure 12, 937-947
9. Eglotf, M. P., Uppenberg, J., Haalck, L. and van Tilbeurgh, H. (2001) Crystal structure of maltose phosphorylase from Lactobacillus brevis: unexpected evolutionary relationship with glucoamylases. Structure 9, 689-697
10. Stam, M. R., Blanc, E., Coutinho, P. M. and Henrissat, B. (2005) Evolutionary and mechanistic relationships between glycosidases acting on α- and β-bonds. Carbohydr. Res. 340, 2728-2734
11. Kitaoka, M., Sasaki, T. and Taniguchi, H. (1992) Synthetic reaction of Cellvibrio gilvus cellobiose phosphorylase. J. Biochem. (Tokyo) 112, 40-44
12. Kitaoka, M., Sasaki, T. and Taniguchi, H. (1992) Conversion of sucrose into cellobiose using sucrose phosphorylase, xylose isomerase and cellobiose phosphorylase. Denpun Kagaku 39, 281-283
13. Kitaoka, M., Sasaki, T. and Taniguchi, H. (1993) Purification and properties of laminaribiose phosphorylase (EC 2.4.1.31) from Euglena gracilis Z. Arch. Biochem. Biophys. 304, 508-514
14. Kitaoka, M., Aoyagi, C. and Hayashi, K. (2001) Colorimetric quantification of cellobiose employing cellobiose phosphorylase. Anal. Biochem. 292, 163-166
15. Liu, A., Tomita, H., Li, H., Miyaki, H., Aoyagi, C., Kaneko, S. and Hayashi, K. (1998) Cloning, sequencing and expression of the cellobiose phosphorylase gene of Cellvibrio gilvus. J. Ferment. Bioeng. 85, 511-513
16. Percy, A., Ono, H., Watt, D. and Hayashi, K. (1998) Synthesis of β-D-glucopyranosyl-(1-4)-D-arabinose, β-D-glucopyranosyl-(1-4)-L- fucose, and β-D-glucopyranosyl-(1-4)-D-altrose catalysed by cellobiose phosphorylase from Cellvibrio gilvus. Carbohydr. Res. 305, 543-548
17. Percy, A., Ono, H. and Hayashi, K. (1998) Acceptor specificity of cellobiose phosphorylase from Cellvibrio gilvus: synthesis of three branched trisaccharides. Carbohydr. Res. 308, 423-429
18. Hidaka, M., Kitaoka, M., Hayashi, K., Wakagi, T., Shoun, H. and Fushinobu, S. (2004) Crystallization and preliminary X-ray analysis of cellobiose phosphorylase from Cellvibrio gilvus. Acta Crystallogr. D Biol. Crystallogr. 60, 1877-1878
19. Otwinowski, Z. and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326
20. Vagin, A. and Teplyakov, A. (1997) MOLREP: an automated program for molecular replacement. J. Appl. Crystallogr. 30, 1022-1025
21. CCP4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50, 760-763
22. Perrakis, A., Morris, R. and Lamzin, V. S. (1999) Automated protein model building combined with iterative structure refinement. Nat. Struct. Biol. 6, 458-463
23. McRee, D. E. (1999) XtalView Xfit-a versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125, 156-165
24. 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. et al. (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54, 905-921
25. Kraulis, P. J. (1991) Molscript - a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946-950
26. Merritt, E. A. and Bacon, D. J. (1997) Raster3D: Photorealistic molecular graphics. Methods Enzymol. 277, 505-524
27. Christopher, J. A. and Baldwin, T. O. (1998) SPOCK: Real-time collaborative molecular modelling. J. Mol. Graphics Model. 16, 285
28. Reference deleted
29. Lu, G. G. (2000) TOP: a new method for protein structure comparisons and similarity searches. J. Appl. Crystallogr. 33, 176-183
30. Lowry, O. H. and Lopez, J. A. (1946) The determination of inorganic phosphate in the presence of labile phosphate esters. J. Biol. Chem. 162, 421-428
31. Kitaoka, M., Sasaki, T. and Taniguchi, H. (1992) Phosphorolytic reaction of Cellvibrio gilvus cellobiose phosphorylase. Biosci. Biotechnol. Biochem. 56, 652-655
32. Nidetzky, B., Eis, C. and Albert, M. (2000) Role of non-covalent enzyme-substrate interactions in the reaction catalysed by cellobiose phosphorylase from Cellulomonas uda. Biochem. J. 351, 649-659
33. Reichenbecher, M., Lottspeich, F. and Bronnenmeier, K. (1997) Purification and properties of a cellobiose phosphorylase (CepA) and a cellodextrin phosphorylase (CepB) from the cellulolytic thermophile Clostridium stercorarium. Eur. J. Biochem. 247, 262-267
34. Kitaoka, M. and Hayashi, K. (2002) Carbohydrate-processing phosphorolytic enzymes. Trends Glycosci. Glycotechnol. 14, 35-50
35. Fushinobu, S., Hidaka, M., Honda, Y., Wakagi, T., Shoun, H. and Kitaoka, M. (2005) Structural basis for the specificity of the reducing end xylose-releasing exo-oligoxylanase from Bacillus halodurans C-125. J. Biol. Chem. 280, 17180-17186
36. Honda, Y., Kitaoka, M. and Hayashi, K. (2004) Reaction mechanism of chitobiose phosphorylase from Vibrio proteolyticus: identification of family 36 glycosyltransferase in Vibrio. Biochem J. 377, 225-232
37. Kitaoka, M., Ogawa, S. and Taniguchi, H. (1993) A cellobiose phosphorylase from Cellvibrio gilvus recognizes only the β-D-form of 5a-carba-glucopyranose. Carbohydr. Res. 247, 355-359
38. Honda, Y., Kitaoka, M. and Hayashi, K. (2003) Reaction mechanism of chitobiose phosphorylase from Vibrio proteolyticus. In Biotechnology of Lignocellulose Degradation and Biomass Utilization (Ohmiya, K., Sakka, K., Karita, S., Kimura, T., Sakka, M. and Onishi, Y., eds.), pp. 484-493, Uni Publishers, Tokyo
39. Street, I. P., Armstrong, C. R. and Withers, S. G. (1986) Hydrogen bonding and specificity. Fluorodeoxy sugars as probes of hydrogen bonding in the glycogen phosphorylase-glucose complex. Biochemistry 25, 6021-6027
40. Honda, Y. and Kitaoka, M. (2004) A family 8 glycoside hydrolase from Bacillus halodurans C-125 (BH2105) is a reducing end xylose-releasing exo-oligoxylanase. J. Biol. Chem. 279, 55097-55103
41. Kim, Y.-K., Kitaoka, M., Krishnareddy, M., Mori, Y. and Hayashi, K. (2002) Kinetic studies of a recombinant cellobiose phosphorylase (CBP) of the Clostridium thermocellum YM4 strain expressed in Escherichia coli. J. Biochem. (Tokyo) 132, 197-203
42. Rajashekhara, E., Kitaoka, M., Kim, Y.-K. and Hayashi, K. (2002) Characterization of a cellobiose phosphorylase from a hyperthermophilic eubacterium, Thermotoga maritima MSB8. Biosci. Biotechnol. Biochem. 66, 2578-2586