Structure-function analysis

  1. Alon Ben-David, Gil Shoham, and Yuval Shoham. A universal screening assay for glycosynthases: Directed evolution of glycosynthase XynB2(E335G) suggests a general path to enhance activity. Chemistry & Biology 15:546-551, 2008.
  2. Alon Ben-David, Tsafrir Bravman, Yael S. Balazs, Mirjam Czjzek, Dietmar Schomburg, Gil Shoham, and Yuval Shoham. Glycosynthase activity of Geobacillus stearothermophilus GH52 -xylosidase: efficient synthesis of xylooligosaccharides from -D-xylopyranosyl fluoride via a conjugated reaction. ChemBioChem 8:2145-2151, 2007.
  3. Anat Alhassid, Alon Ben-David, Orly Tabachnikov, Dima Libster, Einat Naveh, Gennady Zolotnitsky, Yuval Shoham, and Gil Shoham. Crystal structure of an inverting GH43 1,5-α-L-arabinanase from Geobacillus stearothermophilus complexed with its substrate. Biochem. J. 422:73-82, 2009.
  4. Bayer, E. A., L.J.W. Shimon, Y. Shoham, and R. Lamed. Cellulosomes-structure and ultrastructure. J. Structural Biology 124:221-234, 1998.
  5. Berdichevsky, Y., R. Lamed, D. Frenkel, U. Gophna, E. A. Bayer, S. Yaron, Y. Shoham, and I. Benhar. Matrix-assisted refolding of single-chain Fv -cellulose binding domain fusion proteins. Protein Express. Purif. 17:249-259, 1999.
  6. Bravman, Tsfrir, Adva Mechaly, Smadar Shulami, Valery Belakhov, Timor Baasov, Gil Shoham, and Yuval Shoham. Glutamic acid 160 is the acid-base catalyst of ß-xylosidase from Bacillus stearothermophilus T-6: a family 39 glycoside hydrolase.FEBS Lett. 495:115-119, 2001.
  7. Bravman, Tsfrir, Gennady Zolotnitsky, Smadar Shulami, Valery Belakhov, Dmitry Solomon, Timor Baasov, Gil Shoham, and Yuval Shoham. Stereochemistry of family 52 glycosyl hydrolases: a ß-xylosidase from Bacillus stearothermophilus T-6 is a retaining enzyme. FEBS Lett. 495:39-43, 2001
  8. Christian Brüx, Alon Ben-David, Dalia Shallom-Shezifi, Maya Leon, Karsten Niefind, Gil Shoham, Yuval Shoham, Dietmar Schomburg. The structure of an inverting GH43 -xylosidase from Geobacillus stearothermophilus with its substrate reveals the role of the three catalytic residues. J. Mol. Biol. 359:97-109, 2006.
  9. Christian Brux, Karsten Niefind, Alon Ben-David, Maya Leon, Gil Shoham, Yuval Shoham, and Dietmar Schomburg. Crystallization and preliminary crystallographic analysis of a family 43 β-D-xylosidase from Geobacillus stearothermophilus T-6. Acta Cryst F61:1054-1057, 2005
  10. Dalia Shallom, Gali Golan, Gil Shoham and Yuval Shoham. Effect of dimer dissociation on activity and thermostability of the -glucuronidase from Geobacillus stearothermophilus: dissecting the different oligomeric forms of family 67 glycoside hydrolases. J. Bacteriol 186:6928-6937, 2004.
  11. Dalia Shallom, Maya Leon, Tsafrir Bravman, Alon Ben-David, Galia Zaide, Valery Belakhov, Gil Shoham, Dietmar Schomburg, Timor Baasov, and Yuval Shoham. Biochemical characterization and identification of the catalytic residues of a family 43 -D-xylosidase from Geobacillus stearothermophilus T-6. Biochemistry 44:387-397, 2005.
  12. Dalia Shallom, Valery Belakhov, Dmitry Solomon, Gil Shoham, Timor Baasov, and Yuval Shoham. Detailed kinetic Analysis and identification of the nucleophile in -L-arabinofuranosidase from Geobacillus stearothermophilus T-6, a family 51 glycoside hydrolase, J. Biol. Chem 277:43667-43673, 2002.
  13. Dallia Shallom and Yuval Shoham. Microbial Hemicellulases. Curr. Opin. Microbiol.6:219-228, 2003.
  14. Dan Goldman, Noa Lavid, Alon Schwartz, Gil Shoham, Dganit Danino, and Yuval Shoham. Two active forms of Zymomonas mobilis levansucrase: an ordered microfbril strcture of the enzyme promotes levan polymerization. J. Biol. Chem. 283:32209-32217, 2008.
  15. Gali Golan, Dalia Shallom, Anna Teplitsky, Galia Zaide, Smadar Shulami, Timor Baasov, Vivian Stojanoff, Andy Thompson, Yuval Shoham, and Gil Shoham. Crystal structures of Geobacillus stearothermophilus a-glucuronidase complexed with its substrate and products: mechanistic implications. J. Biol.Chem. 279:3014-3024. 2004.
  16. Gennady Zolotnitsky, Uri Cogan, Noam Adir, Vered Solomon, Gil Shoham, and Yuval Shoham. Mapping glycoside hydrolase substrate subsite by isothermal titration calorimetry. Proc. Natl. Acad. Sci. USA 101:11275-11280, 2004.
  17. Gilead S. and Y. Shoham. Purification and characterization of a -L arabinofuranosidase from Bacillus stearothermophilus T-6. Appl. Enviorn. Microbiol. 61:170-174, 1995.
  18. Handelsman, T., and Y. Shoham. Production and characterization of an extracellular thermostable lipase from a Bacillus sp. J. Gen. Appl. Microbiol. 40:435-443, 1994.
  19. Hodaya Solomon, Orly Tabachnikov, Hadar Feinberg, Lata Govada, Naomi Chayen, Yuval Shoham and Gil Shoham. Crystallization and preliminary crystallographic analysis of GanB, an intracellular β-galactosidase from Geobacillus stearothermophilus Acta Cryst F69:1114-1119, 2013.
  20. Klaus Hövel, Dalia Shallom, Karsten Niefind, Timor Baasov, Gil Shoham, Yuval Shoham and Dietmar Schomburg. Crystallization and preliminary X-ray analysis of a family 51 glycoside hydrolase, the -L-arabinofuranosidase from Geobacillus stearothermophilus T-6. Acta Crystallogr. D59:913-915, 2003.
  21. Klaus Hövel, Dalia Shallom, Karsten Niefind, Valery Belakhov, Gil Shoham, Timor Baasov, Yuval Shoham, and Dietmar Schomburg. Crystal structure and snapshots along the reaction pathway of -L-arabinofuranosidase, a family 51 glycosidase. EMBO J. 22:4922-4932, 2003.
  22. Lapidot, A., A. Mechaly, and Y. Shoham. Overexpression and single step purification of a thermostable xylanase from Bacillus stearothermophilus T-6. J. Biotechnol. 51:259-264, 1996.
  23. Liat Bahari, Yuval GIlad, Ilya Borovok, Hamutal Kahel-Raifer, Bareket Dassa, Yakir Nataf, Yuval Shoham, Raphael Lamed, Edward A. Bayer. Glycoside hydrolases as components of putative carbohydrate biosensor proteins in Clostridium thermocellum J. Ind. Microbiol. Biotechnol. 38:825–832, 2011.
  24. Maya Bar, Gali Golan, Magda Nechama, Gennady Zolotnitsky, Yuval Shoham, and Gil Shoham. A new crystal form of XT6, enables a significant improvement of its diffraction quality and resolution. Acta Crystallogr. D60:545-549. 2004.
  25. Mechaly, A., A. Teplitsky, V. Belakhov, T. Baasov, G. Shoham and Y. Shoham. Overproduction and characterization of seleno-methionine xylanase T-6. J. Biotechnol. 78:83-86, 2000
  26. Mechaly, A., V. Belakhov, Y. Shoham, and T. Baasov. An efficient chemical – enzymatic synthesis of 4-nitrophenyl ß-xylobioside: a chromogenic substrate for xylanases. Carbohydr. Res. 304:111-115, 1997.
  27. Mirjam Czjzek, Alon Ben David, Tsafrir Bravman, Gil Shoham, Bernard Henrissat, and Yuval Shoham. Enzyme-substrate complex structures of a GH39 β-xylosidase from Geobacillus stearothermophilus. J. Mol. Biol. 353:838-846, 2005.
  28. Mirjam Czjzek, Tsafrir Bravman, Bernard Henrissat, and Yuval Shoham. Crystallization and preliminary crystallographic analysis of a thermostable family 52 -D-xylosidase from Geobacilluss stearothermophilus T-6. Acta Crystallogr. D60:1461-1463, 2004.
  29. Mirjam Czjzek, Tsafrir Bravman, Bernard Henrissat, Yuval Shoham. Crystallization and preliminary X-ray analysis of family 39 -D-xylosidase from Geobacillus stearothermophilus T-6. Acta Crystallogr. D60:583-585. 2004.
  30. Onit Alalouf, Yael Balazs, Margarita Volkinshtein, Yael Grimpel, Gil Shoham, Yuval Shoham.A new family of carbohydrate esterases is represented by a GDSL/acetylxylan esterase from Geobacillus stearothermophilus.J. Biol.Chem. 286:41993-42001, 2011.
  31. Oren Yaniv, Galit Fichman, Ilya Borovok, Yuval Shoham, Edward Bayer, Raphael Lamed, Linda Shimon and Felix Frolow. Fine-structural variance of family 3 carbohydrate-binding modules as extracellular biomass-sensing components of Clostridium thermocellum anti-sigmaI factors. Acta Cryst D70: 522-534, 2014.
  32. Orly Tabachnikov and Yuval Shoham. Functional Characterization of the Galactan Utilization System of Geobacillus stearothermophilus. FEBS J 280:950-964, 2013.
  33. Öznur Kökpinar, Johanna-Gabriela Walter, Yuval Shoham, Frank Stahl, and Thomas Scheper. Aptamer-based downstream processing of His-tagged proteins utilizing magnetic beads. Biotechnol. Bioeng. 108:2371-2379, 2011.
  34. Rachel Salama, Onit Alalouf, Orly Tabachnikov, Gennady Zolotnitsky, Gil Shoham, Yuval Shoham. The abp gene in Geobacillus stearothermophilus T-6 encodes a GH27 β-L-arabinopyranosidase. FEBS Lett. 586:2436–2442, 2012.
  35. Reiland, V., Fundoiano-Hershcovitz, Y., Golan, G., Gilboa, R., Shoham, Y. and Shoham, G. Preliminary crystallographic characterization of SGAP, an extracellular aminopeptidase from Bacillus subtilis, Acta Cryst. D60:2371-2376, 2004.
  36. Reiland, V., R. Gilboa, A. Spungin-Bialik, D. Schomburg, Y. Shoham, S. Blumberg, and G. Shoham. Binding of inhibitory aromatic amino acids to Streptomyces griseus aminopeptidase. Acta Crystallogr. D60:1738-1746, 2004.
  37. Roie Dann, Shifra Lansky, Noa Lavid, Arik Zehavi, Valery Belakhov, Timor Baasov, Babu Manjasetty, Hassan Belrhali, Yuval Shoham and Gil Shoham. Preliminary crystallographic analysis of Xyn52B2, a GH52 [beta]-D-xylosidase from Geobacillus stearothermophilus T6 (submitted).
  38. Sadanari Jindou, Qi Xu, Rina Kenig, Michal Shulman, Yuval Shoham, Edward Bayer, and Raphael Lamed. Novel architecture of family-9 glycoside hydrolases identified in cellulosomal enzymes of Acetivibrio cellulolyticus and Clostridium thermocellum. FEMS Lett. 254:308-316, 2006.
  39. Sarah Moraïs, Orly Salama-Alber, Yoav Baraka, Yitzhak Hadar, David B. Wilson, Raphael Lamed, Yuval Shoham and Edward A. Bayer. Functional association of the catalytic and ancillary modules dictates enzymatic activity in a family-43 -xylosidase. J. Biol. Chem. 287:9213-9221, 2012.
  40. Sarah Moraïs, Yoav Barak, Yitzhak Hadar, David Wilson, Yuval Shoham, Raphael Lamed, and Edward Bayer. Assembly of xylanases into designer cellulosomes promotes efficient hydrolysis of the xylan component of a natural recalcitrant cellulosic substrate. MBio 2(6):e00233-11, 2011.
  41. Sarah Moraïsa, Yoav Barak, Jonathan Caspia, Yitzhak Hadar, Raphael Lamed, Yuval Shoham, David B. Wilson, and Edward A. Bayer. Cellulase-xylanase synergy in designer cellulosome for enhanced degradation of a complex cellulosic substrate. mBio 1(5):e00285-10. doi:10.1128/mBio.00285-10, 2010.
  42. Shallom Dalia, Valery Belakhov, Dmitry Solomon, Sara Gilead-Gropper, Timor Baasov, Gil Shoham, and Yuval Shoham The identification of the acid-base catalyst of alpha-arabinfuranosidase from Bacillus stearothermophilus T-6, a family 51 glycoside hydrolase.FEBS Lett. 514:163-167, 2002.
  43. Shifra Lansky, Arik Zehavi, Roie Dann, Hay Dvir, Hassan Belrhali, Yuval Shoham and Gil Shoham. Purification, crystallization and preliminary crystallographic analysis of Gan1D, a GH1 6-phospho-β-galactosidase from Geobacillus stearothermophilus. Acta Cryst F70:225-231, 2014.
  44. Shifra Lansky, Onit Alalouf, Rachel Salama, Hay Dvir, Yuval Shoham and Gil Shoham. Preliminary crystallographic analysis of a double mutant of the acetyl xylo-oligosaccharide esterase Axe2 in its dimeric form. Acta Cryst F70:476–481, 2014.
  45. Shifra Lansky, Onit Alalouf, Vered Solomon, Anat Alhassid, Lata Govada, Naomi Chayan, Hassan Belrhali, Yuval Shoham and Gil Shoham. Crystallization and preliminary crystallographic analysis of Axe2, an acetylxylan esterase from Geobacillus stearothermophilus. Acta Cryst F69, 430–434, 2013.
  46. Shifra Lansky, Onit Alalouf, Vered Solomon, Anat Alhassid, Lata Govada, Naomi Chayen, Hassan Belrhali, Yuval Shoham and Gil Shoham. A unique octameric structure of Axe2, an intracellular acetyl-xylooligosaccharide esterase from Geobacillus stearothermophilus. Acta Cryst D70:261-278, 2014.
  47. Shifra Lansky, Rachel Salama, Hodaya V. Solomon, Hadar Feinberg, Hassan Belrhali, Yuval Shoham and Gil Shoham. Structure-specificity relationships in Abp, a GH27 β-L-arabinopyranosidase from Geobacillus stearothermophilus. Acta Cryst D (accepted).
  48. Shifra Lansky, Rachel Salama, Roie Dann, Izhak Shner, Babu Manjasetty, Hasan Belrhali, Yuval Shoham and Gil Shoham.Cloning, purification and preliminary crystallographic analysis of Ara127N, a GH127 β-L-arabinofuranosidase from Geobacillus stearothermophilus T6 Acta Cryst F70:1038–1045, 2014.
  49. Shifra Lansky, Rachel Salama, Vered Solomon, Hassan Belrhali, Yuval Shoham and Gil Shoham. Crystallization and preliminary crystallographic analysis of Abp, a GH27 β-L-arabinopyranosidase from G. Stearothermophilus. Acta Cryst F69:695-699, 2013.
  50. Solomon, V., A. Teplitsky, S. Shulami, G. Zolotnitsky, Y. Shoham, and G. Shoham. Structure-specificity relationships of an intracellular xylanase from Geobacillus stearothermophilus. Acta Cryst. D63:845-859, 2007.
  51. Tal Burstein, Michal Shulman, Sadanari Jindou, Svetlana Petkun, Felix Frolow, Yuval Shoham, Edward A. Bayer, and Raphael Lamed. Physical association of the catalytic and helper modules of a family-9 glycoside hydrolase is essential for activity. FEBS Lett. 583:879-884, 2009.
  52. Teplitsky, A. Mechaly, V. Stojanoff, G. Sainz, G. Golan, H. Feinberg, R. Gilboa1, V. Reiland, G. Zolotnitsky, D. Shallom, A. Thompson, Y. Shoham & G. Shoham. Structure determination of the extracellular xylanase from Geobacillus stearothermophilus by selenomethionyl MAD phasing. Acta Crystallogr. D60:836-848. 2004.
  53. Teplitsky, A., H. Feinberg, R. Gilboa, A. Lapidot, A. Mechaly, V. Stojanoff, M. Capel, Y. Shoham, and G. Shoham. Crystallization and preliminary crystallographic analysis of the thermostable, alkaline tolerant xylanase from Bacillus stearothermophilus T-6. Acta Crystallogr. D. 53:608-611, 1997.
  54. Teplitsky, A., S. Shulami, S. Moryles, G. Zaide, Y. Shoham, and G. Shoham. Crystalization and preliminary X-ray analysis of -D-glucuronidase from Bacillus stearothemophilus T-6. Acta Crystallogr. D55:869-872, 1999.
  55. Teplitsky, A., S. Shulami, S. Moryles, Y. Shoham, and G. Shoham. Crystallization and preliminary X-ray analysis of an intracellular xylanase from Bacillus stearothermophilus T-6. Acta Crystallogr. D56, 181-184, 2000.
  56. Tsafrir Bravman, Gennady Zolotnitsky, Valery Belakhov, Timor Baasov, Gil Shoham, Bernard Henrissat, and Yuval Shoham. Detailed kinetic analysis of a family 52 glycoside hydrolase: a -xylosidase from Geobacillus stearothermophilus. Biochemistry 42:10528-10536, 2003.
  57. Tsafrir Bravman, Valery Belakhov, Dmitry Solomon, Gil Shoham, Bernard Henrissat, Timor Baasov and Yuval Shoham. Identification of the catalytic residues in family 52 glycoside hydrolase, a -xylosidase from Geobacillus stearothermophilus T-6. J. Biol. Chem. 278:26742-26749, 2003.
  58. Yael Balazs, Elina Lisitsin, Oshrat Carmiel, Gil Shoham, Yuval Shoham, and Asher Schmidt. Identifying critical unrecognized sugar – protein interactions in GH10 xylanases from Geobacillus stearothermophilus using STD NMR. FEBS Journal 280:4652–4665, 2013.
  59. Yifat Fundoiano-Hershcovitz, Larisa Rabinovitch, Smadar Shulami, Vera Reiland, Gil Shoham, and Yuval Shoham. The ywad gene from Bacillus subtilis encodes for a double-zinc aminopeptidase. FEMS Lett. 243:157-163, 2005.
  60. Yifat Fundoiano-Hershcovitz, Larisa Rabinovitch, Yael Langut, Vera Reiland Gil Shoham, and Yuval Shoham. Identification of the catalytic residues in the double zinc aminopeptidase from Streptomyces griseus. FEBS Lett. 571:192-196, 2004
  61. Yifat Fundoiano-Hershcovitz, Rotem Gilboa, Vera Reiland, Gil Shoham and Yuval Shoham. Catalytic mechanism of SGAP, a double-zinc aminopeptidase from Streptomyces griseus. FEBS J. 274:3864–3876, 2007.
  62. Zaide Galia, Dalia Shallom, Smadar Shulami, Gennady Zolotnitsky, Gali Golan, Anna Teplitsky, Timor Baasov, Gil Shoham, and Yuval Shoham. Biochemical characterization and identification of catalytic residues in -glucuronidase from Bacillus stearothermophilus T-6. Eur. J. Biochem. 268:3006-3016, 2001.