The crystal structure of rice (Oryza sativa L.) Os4BGlu12, an oligosaccharide and tuberonic acid glucoside-hydrolyzing β-glucosidase with significant thioglucohydrolase activity

Archives of Biochemistry and Biophysics

Volumn 510, Issue 1, 2011, Pages 62-72

  Sansenya, Sompong ^a   Opassiri, Rodjana ^a   Kuaprasert, Buabarn ^b   Chen, Chun Jung ^c   Ketudat Cairns, James R ^a  

^a SURANAREE UNIVERSITY OF TECHNOLOGY   (Thailand)

^b SYNCHROTRON LIGHT RESEARCH INSTITUTE   (Thailand)

^c NATIONAL SYNCHROTRON RADIATION RESEARCH CENTER   (Taiwan)

Author keywords

Covalent intermediate; Glycoside hydrolase; Michaelis complex; Rice; Substrate specificity; X ray crystallography

Indexed keywords

BETA GLUCOSIDASE; GLUCOSIDE; GLYCOSIDASE; HYDROLASE; NUCLEOPHILE; OLIGOSACCHARIDE; OS4BGLU12 ENZYME; THIOGLUCOHYDROLASE; TUBERONIC ACID GLUCOSIDE; UNCLASSIFIED DRUG;

ARTICLE; CHEMICAL BOND; COMPARATIVE STUDY; COMPLEX FORMATION; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME CONFORMATION; ENZYME STABILITY; ENZYME STRUCTURE; HYDROLYSIS; LIGAND BINDING; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RICE;

BETA-GLUCOSIDASE; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; CYCLOPENTANES; ENZYME STABILITY; GLUCOSIDES; HYDROLYSIS; MODELS, MOLECULAR; OLIGOSACCHARIDES; ORYZA SATIVA; PROTEIN BINDING; SUBSTRATE SPECIFICITY;

ORYZA SATIVA;

EID: 79955904349     PISSN: 00039861     EISSN: 10960384     Source Type: Journal    
DOI: 10.1016/j.abb.2011.04.005     Document Type: Article

References (55)

1. B. Henrissat Biochem. J. 280 1991 309 316
2. B.L. Cantarel, P.M. Coutinho, C. Rancurel, T. Thomas Bernard, V. Vincent Lombard, and B. Henrissat Nucleic Acids Res. 37 2009 233 238
3. J.R. Ketudat Cairns, and A. Esen Cell. Mol. Life Sci. 67 2010 3389 3405
4. Z. Xu, L.L. Escamilla-Treviño, L. Zeng, M. Lalgondar, D.R. Bevan, B.S.J. Winkel, A. Mohamed, C.L. Cheng, M.C. Shih, J.E. Poulton, and A. Esen Plant Mol. Biol. 55 2004 343 367
5. R. Opassiri, B. Pomthong, T. Onkoksoong, T. Akiyama, A. Esen, and J.R. Ketudat Cairns BMC Plant Biol. 6 2006 33
6. J. Jenkins, L.L. Leggio, G. Harris, and R. Pickersgill FEBS Lett. 362 1995 281 285
7. B. Henrissat, I. Callebaut, S. Fabrega, P. Lehn, J.P. Mornon, and G. Davies Proc. Natl. Acad. Sci. USA 92 1995 7090 7094
8. S.G. Withers, R.A.J. Warren, I.P. Street, K. Rupitz, J.B. Kempton, and R. Aebersold J. Am. Chem. Soc. 112 1990 5887 5889
9. T. Barrett, C.G. Suresh, S.P. Tolley, E.J. Dodson, and M.A. Hughes Structure 5 1995 951 960
10. W.P. Burmeister, S. Cottaz, H. Driguez, R. Iori, S. Palmieri, and B. Henrissat Structure 5 1997 663 675
11. W.P. Burmeister, S. Cottaz, P. Rollin, A. Vasella, and B. Henrissat J. Biol. Chem. 275 2000 30385 39393
12. H. Husebye, S. Arzt, W.P. Burmeister, F.V. Haertel, A. Brandt, J.T. Rossiter, and A.M. Bones Insect. Biochem. Mol. Biol. 35 2005 1311 1320
13. G.J. Davies, V.M.-A. Ducros, A. Varrot, and D.L. Zechel Biochem. Soc. Trans. 31 2003 523 527
14. D.L. Zechel, A.B. Boraston, T. Gloster, C.M. Boraston, J.M. Macdonald, D.M. Tilbrook, R.V. Stick, and G.J. Davies J. Am. Chem. Soc. 125 2003 14313 14323
15. T.M. Gloster, S. Roberts, V.M. Ducros, G. Perugino, M. Rossi, R. Hoos, M. Moracci, A. Vasella, and G.J. Davies Biochemistry 43 2004 6101 6109
16. W. Chuenchor, S. Pengthaisong, R.C. Robinson, J. Yuvaniyama, W. Oonanant, D.R. Bevan, A. Esen, C.J. Chen, R. Opassiri, J. Svasti, and J.R. Ketudat Cairns J. Mol. Biol. 377 2008 1200 1215
17. S. Seshadri, T. Akiyama, R. Opassiri, B. Kuaprasert, and J.R. Ketudat Cairns Plant Physiol. 151 2009 47 58
18. J. Noguchi, Y. Hayashi, Y. Baba, O. Zkino, and M. Kimura Biochem. Biophys. Res. Comm. 374 2008 549 552
19. L. Verdoucq, J. Morinire, D.R. Bevan, A. Esen, A. Vasella, B. Henrissat, and M. Czjzek J. Biol. Chem. 279 2004 31796 31803
20. M. Czjzek, M. Cicek, V. Zamboni, W.P. Burmeister, D.R. Bevan, B. Henrissat, and A. Esen Proc. Natl. Acad. Sci. USA 97 2000 13555 13560
21. M. Sue, K. Yamazaki, S. Yajima, T. Nomura, T. Matsukawa, H. Iwamura, and T. Miyamoto Plant Physiol. 141 2006 1237 1247
22. M. Sue, C. Nakamura, T. Miyamoto, and S. Yajima Plant Sci. 180 2011 268 275
23. L. Barleben, S. Panjikar, M. Ruppert, J. Koepke, and J. Stöckigt Plant Cell 19 2007 2886 2897
24. M. Cicek, and A. Esen Biotechnol. Bioeng. 63 1999 392 400
25. T. Akiyama, H. Kaku, and N. Shibuya Phytochemistry 48 1998 49 54
26. R. Opassiri, J. Maneesan, T. Akiyama, B. Pomthong, S. Jin, A. Kimura, and J.R. Ketudat Cairns Plant Sci. 179 2010 273 280
27. R. Opassiri, Y. Hua, O. Wara-Aswapati, T. Akiyama, J. Svasti, A. Esen, and J.R. Ketudat Cairns Biochem. J. 379 2004 125 131
28. T. Kuntothom, S. Luang, A.J. Harvey, G.B. Fincher, R. Opassiri, M. Hrmova, and J.R. Ketudat Cairns Arch. Biochem. Biophys. 491 2009 85 95
29. S. Wakuta, S. Hamada, H. Ito, H. Matsuura, K. Nabeta, and H. Matsui Phytochemistry 71 2010 1280 1288
30. S. Wakuta, S. Hamada, H. Ito, R. Imai, H. Mori, H. Matsuura, K. Nabeta, and H. Matsui J. Appl. Glycosci. 58 2011 67 70
31. S. Sansenya, J.R. Ketudat Cairns, and R. Opassiri Acta Crystallogr. F66 2010 320 323
32. Z. Otwinowski, and W. Minor Meth. Enzymol. Academic Press, New York 276 1997 307 326
33. A. Vagin, and A. Teplyakov J. Appl. Crystallogr. 30 1997 1022 1025
34. G.N. Murdushov, A.A. Vagin, A. Lebedev, K.S. Wilson, and E.J. Dodson Acta Crystallogr. D55 1999 247 255
35. P. Emsley, and K. Cowtan Acta Crystallogr. D60 2004 2126 2132
36. R.A. Laskowski, M.W. MacArthur, D.S. Moss, and J.M. Thornton J. Appl. Crystallogr. 26 1993 283 291
37. I.W. Davis, A. Leaver-Fay, V.B. Chen, J.N. Block, G.J. Kapral, X. Wang, L.W. Murray, W.B. Arendall, J. Snoeyink, J.S. Richardson, and D.C. Richardson Nucleic Acids Res. 35 2007 375 383
38. W.L. Delano, The Pymol Molecular Graphics System (2002) (Online). Available from: < http://www.pymol.org/ >.
39. R. Opassiri, J.R. Ketudat-Cairns, T. Akiyama, O. Wara-Aswapati, J. Svasti, and A. Esen Plant Sci. 165 2003 627 638
40. M. Dixon Biochem. J. 55 1953 170 171
41. W. Chuenchor, S. Pengthaisong, R.C. Robinson, J. Yuvaniyama, and J. Svasti J. Struct. Biol. 173 2011 169 179
42. M. Czjzek, M. Cicek, V. Zamboni, W.P. Burmeister, D.R. Bevan, B. Henrissat, and A. Esen Biochem. J. 354 2001 37 46
43. V. Rotrekl, E. Nejedla, I. Kucera, F. Abdallah, K. Palme, and B. Brzobohaty Eur. J. Biochem. 266 1999 1056 1065
44. J.J. Tanner, R.M. Hecht, and K.L. Krause Biochemistry 35 1996 2597 2609
45. E. Krissinel, and K. Henrick J. Mol. Biol. 372 2007 774 797
46. P. Isorna, J. Polaina, L. Latorre-García, F.J. Cañada, B. González, and J. Sanz-Aparicio J. Mol. Biol. 371 2007 1204 1218
47. C. Malet, and A. Planas FEBS Lett. 440 1998 208 212
48. M. Okuyama, H. Mori, K. Watanabe, A. Kimura, and S. Chiba Biosci. Biotechnol. Biochem. 66 2002 928 933
49. G. Hommalai, S.G. Withers, W. Chuenchor, J.R. Ketudat Cairns, and J. Svasti Glycobiology 17 2007 744 753
50. H. Shen, and L.D. Byers Biochem. Biophys. Res. Commun. 362 2007 717 720
51. T. Kuntothom, M. Raab, I. Tvaroska, S. Fort, S. Pengthaisong, F.J. Cañada, L. Calle, J. Jimenez-Barbero, J.R. Ketudat Cairns, and M. Hrmova Biochemistry 49 2010 8779 8793
52. M. Wang, D. Lee, X. Sun, Y.J. Zhu, H. Nong, and J. Zhang Plant Sci. 177 2009 716 723
53. K. Tamura, J. Dudley, M. Nei, and S. Kumar Mol. Biol. Evol. 24 2007 1596 1599
54. M. Nei, and S. Kumar Molecular Evolution and Phylogenetics 2000 Oxford University Press New York
55. R.C. Edgar Nucleic Acids Res. 32 2004 1792 1797