A unique octameric structure of Axe2, an intracellular acetyl- xylooligosaccharide esterase from Geobacillus stearothermophilus

Acta Crystallographica Section D: Biological Crystallography

Volumn 70, Issue 2, 2014, Pages 261-278

  Lansky, Shifra ^a   Alalouf, Onit ^b   Solomon, Hodaya Vered ^a   Alhassid, Anat ^a   Govada, Lata ^c   Chayen, Naomi E ^c   Belrhali, Hassan ^d   Shoham, Yuval ^b   Shoham, Gil ^a  

^a HEBREW UNIVERSITY OF JERUSALEM   (Israel)

^b TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

^c IMPERIAL COLLEGE LONDON   (United Kingdom)

^d EUROPEAN SYNCHROTRON RADIATION FACILITY   (France)

Author keywords

catalytic triad; Geobacillus stearothermophilus; octamer; oligomeric assembly; SAD data collection; SAXS; serine esterases; torus; xylooligosaccharide esterases

Indexed keywords

ACETYLESTERASE; ACETYLXYLAN ESTERASE; BACTERIAL PROTEIN; GLUCURONIC ACID; OCTAMER; OLIGOSACCHARIDE; RECOMBINANT PROTEIN; XYLOOLIGOSACCHARIDE;

ARTICLE; BIOCATALYSIS; CATALYTIC TRIAD; CHEMICAL STRUCTURE; CHEMISTRY; ENZYME ACTIVE SITE; ENZYME SPECIFICITY; ENZYMOLOGY; GENETICS; GEOBACILLUS STEAROTHERMOPHILUS; KINETICS; MUTATION; OLIGOMERIC ASSEMBLY; PROTEIN MULTIMERIZATION; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; SAD DATA COLLECTION; SAXS; SERINE ESTERASES; STATIC ELECTRICITY; STRUCTURE ACTIVITY RELATION; TORUS; X RAY CRYSTALLOGRAPHY; XYLOOLIGOSACCHARIDE ESTERASES;

CATALYTIC TRIAD; GEOBACILLUS STEAROTHERMOPHILUS; OCTAMER; OLIGOMERIC ASSEMBLY; SAD DATA COLLECTION; SAXS; SERINE ESTERASES; TORUS; XYLOOLIGOSACCHARIDE ESTERASES;

ACETYLESTERASE; BACTERIAL PROTEINS; BIOCATALYSIS; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; GEOBACILLUS STEAROTHERMOPHILUS; GLUCURONATES; KINETICS; MODELS, MOLECULAR; MUTATION; OLIGOSACCHARIDES; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; RECOMBINANT PROTEINS; STATIC ELECTRICITY; STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY;

EID: 84894206753     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S139900471302840X     Document Type: Article

References (70)

1. Akoh, C. C., Lee, G.-C., Liaw, Y.-C., Huang, T.-H. & Shaw, J.-F. (2004). Prog. Lipid Res. 43, 534-552.
2. Alalouf, O., Balazs, Y., Volkinshtein, M., Grimple, Y., Shoham, G. & Shoham, Y. (2011). J. Biol. Chem. 286, 41993-42001.
3. Allaire, M. & Yang, L. (2011). J. Synchrotron Rad. 18, 41-44.
4. Aspinall, G. O. (1959). Adv. Carbohydr. Chem. 1, 429-468.
5. Banacký, P. & Linder, B. (1981). Biophys. Chem. 13, 223-231.
6. Bar, M., Golan, G., Nechama, M., Zolotnitsky, G., Shoham, Y. & Shoham, G. (2004). Acta Cryst. D60, 545-549.
7. Ben-David, A., Bravman, T., Balazs, Y. S., Czjzek, M., Schomburg, D., Shoham, G. & Shoham, Y. (2007). Chembiochem, 8, 2145-2151.
8. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N. & Bourne, P. E. (2000). Nucleic Acids Res. 28, 235-242.
9. Biely, P. (2012). Biotechnol. Adv. 30, 1575-1588.
10. Bitto, E., Bingman, C. A., McCoy, J. G., Allard, S. T. M., Wesenberg, G. E. & Phillips, G. N. (2005). Acta Cryst. D61, 1655-1661.
11. Bouveng, H. O. (1961). Acta Chem. Scand. 15, 96-100.
12. Bravman, T., Mechaly, A. G., Shulami, S., Belakhov, V., Baasov, T., Shoham, G. & Shoham, Y. (2001). FEBS Lett. 495, 115-119.
13. Bravman, T., Zolotnitsky, G., Belakhov, V., Shoham, G., Henrissat, B., Baasov, T. & Shoham, Y. (2003). Biochemistry, 42, 10528-10536.
14. Bravman, T., Zolotnitsky, G., Shulami, S., Belakhov, V., Solomon, D., Baasov, T., Shoham, G. & Shoham, Y. (2001). FEBS Lett. 495, 39-43.
15. Brüx, C., Ben-David, A., Shallom-Shezifi, D., Leon, M., Niefind, K., Shoham, G., Shoham, Y. & Schomburg, D. (2006). J. Mol. Biol. 359, 97-109.
16. Cantarel, B. L., Coutinho, P. M., Rancurel, C., Bernard, T., Lombard, V. & Henrissat, B. (2009). Nucleic Acids Res. 37, D233-D238.
17. Czjzek, M., Bravman, T., Henrissat, B. & Shoham, Y. (2004). Acta Cryst. D60, 1461-1463.
18. Devenish, S. R. A. & Gerrard, J. A. (2009). Org. Biomol. Chem. 7, 833-839.
19. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. (2010). Acta Cryst. D66, 486-501.
20. Engh, R. A. & Huber, R. (1991). Acta Cryst. A47, 392-400.
21. Finn, R. D., Mistry, J., Tate, J., Coggill, P., Heger, A., Pollington, J. E., Gavin, O. L., Gunasekaran, P., Ceric, G., Forslund, K., Holm, L., Sonnhammer, E. L., Eddy, S. R. & Bateman, A. (2010). Nucleic Acids Res. 38, D211-D222.
22. Gat, O., Lapidot, A., Alchanati, I., Regueros, C. & Shoham, Y. (1994). Appl. Environ. Microbiol. 60, 1889-1896.
23. Golan, G., Shallom, D., Teplitsky, A., Zaide, G., Shulami, S., Baasov, T., Stojanoff, V., Thompson, A., Shoham, Y. & Shoham, G. (2004). J. Biol. Chem. 279, 3014-3024.
24. Griffin, M. D. W. & Gerrard, J. A. (2012). Adv. Exp. Med. Biol. 747, 74-90.
25. Guinier, A. (1939). Ann. Phys. 12, 161.
26. Holm, L. & Sander, C. (1995). Trends Biochem. Sci. 20, 478-480.
27. Hövel, K., Shallom, D., Niefind, K., Belakhov, V., Shoham, G., Baasov, T., Shoham, Y. & Schomburg, D. (2003). EMBO J. 22, 4922-4932.
28. Khasin, A., Alchanati, I. & Shoham, Y. (1993). Appl. Environ. Microbiol. 59, 1725-1730.
29. Konarev, P. V., Petoukhov, M. V., Volkov, V. V. & Svergun, D. I. (2006). J. Appl. Cryst. 39, 277-286.
30. Konarev, P. V., Volkov, V. V., Sokolova, A. V., Koch, M. H. J. & Svergun, D. I. (2003). J. Appl. Cryst. 36, 1277-1282.
31. Kozin, M. B. & Svergun, D. I. (2001). J. Appl. Cryst. 34, 33-41.
32. Krissinel, E. & Henrick, K. (2007). J. Mol. Biol. 372, 774-797.
33. Lamzin, V. S. & Wilson, K. S. (1993). Acta Cryst. D49, 129-147.
34. Lansky, S., Alalouf, O., Solomon, V., Alhassid, A., Govada, L., Chayan, N. E., Belrhali, H., Shoham, Y. & Shoham, G. (2013). Acta Cryst. F69, 430-434.
35. Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. (1993). J. Appl. Cryst. 26, 283-291.
36. Lapidot, A., Mechaly, A. & Shoham, Y. (1996). J. Biotechnol. 51, 259-264.
37. Lee, Y.-L., Lee, L.-C. & Shaw, J.-F. (2012). Biocatal. Agric. Biotechnol. 1, 95-104.
38. Levisson, M. et al. (2012). Proteins, 80, 1545-1559.
39. Lindberg, B., Rosell, K.-G. & Svensson, S. (1973a). Sven. Papperstidn. 76, 30-32.
40. Lindberg, B., Rosell, K.-G. & Svensson, S. (1973b). Sven. Papperstidn. 76, 383-384.
41. Luzzati, V. (1952). Acta Cryst. 5, 802-810.
42. Mathews, I., Soltis, M., Saldajeno, M., Ganshaw, G., Sala, R., Weyler, W., Cervin, M. A., Whited, G. & Bott, R. (2007). Biochemistry, 46, 8969-8979.
43. Matthews, J. M. & Sunde, M. (2012). Adv. Exp. Med. Biol. 747, 1-18.
44. Mølgaard, A., Kauppinen, S. & Larsen, S. (2000). Structure, 8, 373-383.
45. Montoro-García, S., Gil-Ortiz, F., García-Carmona, F., Polo, L. M., Rubio, V. & Sánchez-Ferrer, Á. (2011). Biochem. J. 436, 321-330.
46. Murshudov, G. N., Skubák, P., Lebedev, A. A., Pannu, N. S., Steiner, R. A., Nicholls, R. A., Winn, M. D., Long, F. & Vagin, A. A. (2011). Acta Cryst. D67, 355-367.
47. Pape, T. & Schneider, T. R. (2004). J. Appl. Cryst. 37, 843-844.
48. Petoukhov, M. V., Franke, D., Shkumatov, A. V., Tria, G., Kikhney, A. G., Gajda, M., Gorba, C., Mertens, H. D. T., Konarev, P. V. & Svergun, D. I. (2012). J. Appl. Cryst. 45, 342-350.
49. Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C. & Ferrin, T. E. (2004). J. Comput. Chem. 25, 1605-1612.
50. Ramachandran, G. N., Sasisekharan, V. & Ramakrishnan, C. (1963). J. Mol. Biol. 7, 95-99
51. Shallom, D., Belakhov, V., Solomon, D., Gilead-Gropper, S., Baasov, T., Shoham, G. & Shoham, Y. (2002). FEBS Lett. 514, 163-167.
52. Shallom, D., Belakhov, V., Solomon, D., Shoham, G., Baasov, T. & Shoham, Y. (2002). J. Biol. Chem. 277, 43667-43673.
53. Shallom, D., Golan, G., Shoham, G. & Shoham, Y. (2004). J. Bacteriol. 186, 6928-6937.
54. Shallom, D., Leon, M., Bravman, T., Ben-David, A., Zaide, G., Belakhov, V., Shoham, G., Schomburg, D., Baasov, T. & Shoham, Y. (2005). Biochemistry, 44, 387-397.
55. Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.
56. Sheldrick, G. M. (2010). Acta Cryst. D66, 479-485.
57. Shulami, S., Gat, O., Sonenshein, A. L. & Shoham, Y. (1999). J. Bacteriol. 181, 3695-3704.
58. Shulami, S., Zaide, G., Zolotnitsky, G., Langut, Y., Feld, G., Sonenshein, A. L. & Shoham, Y. (2007). Appl. Environ. Microbiol. 73, 874-884.
59. Solomon, V., Teplitsky, A., Shulami, S., Zolotnitsky, G., Shoham, Y. & Shoham, G. (2007). Acta Cryst. D63, 845-859.
60. Svergun, D. I. (1999). Biophys. J. 76, 2879-2886.
61. Svergun, D., Barberato, C. & Koch, M. H. J. (1995). J. Appl. Cryst. 28, 768-773.
62. Tabachnikov, O. & Shoham, Y. (2013). FEBS J. 280, 950-964.
63. Vincent, F., Charnock, S. J., Verschueren, K. H. G., Turkenburg, J. P., Scott, D. J., Offen, W. A., Roberts, S., Pell, G., Gilbert, H. J., Davies, G. J. & Brannigan, J. A. (2003). J. Mol. Biol. 330, 593-606.
64. Volkov, V. V. & Svergun, D. I. (2003). J. Appl. Cryst. 36, 860-864.
65. Wei, Y., Schottel, J. L., Derewenda, U., Swenson, L., Patkar, S. & Derewenda, Z. S. (1995). Nature Struct. Biol. 2, 218-223.
66. Winn, M. D. et al. (2011). Acta Cryst. D67, 235-242.
67. Yang, L. (2010). SAXS/WAXS Data Collection at X9. SAXS Workbench. Brookhaven National Laboratory, New York, USA.
68. Zaide, G., Shallom, D., Shulami, S., Zolotnitsky, G., Golan, G., Baasov, T., Shoham, G. & Shoham, Y. (2001). Eur. J. Biochem. 268, 3006-3016.
69. Zhang, J., Siika-Aho, M., Tenkanen, M. & Viikari, L. (2011). Biotechnol. Biofuels, 4, 60.
70. Zolotnitsky, G., Cogan, U., Adir, N., Solomon, V., Shoham, G. & Shoham, Y. (2004). Proc. Natl Acad. Sci. USA, 101, 11275-11280.