Retaining glycosyl hydrolases, which catalyse both glycosylation and deglycosylation in a concerted manner, are the most abundant hydrolases. To date, their visualization has tended to be focused on glycosylation because glycosylation reactions can be visualized by inactivating deglycosylation step and/or using substrate analogues to isolate covalent intermediates ...
Retaining glycosyl hydrolases, which catalyse both glycosylation and deglycosylation in a concerted manner, are the most abundant hydrolases. To date, their visualization has tended to be focused on glycosylation because glycosylation reactions can be visualized by inactivating deglycosylation step and/or using substrate analogues to isolate covalent intermediates. Furthermore, during structural analyses of glycosyl hydrolases with hydrolytic reaction products by the conventional soaking method, mutarotation of an anomeric carbon in the reaction products promptly and certainly occurs. This undesirable structural alteration hinders visualization of the second step in the reaction. Here, we investigated X-ray crystallographic visualization as a possible method for visualizing the conformational itinerary of a retaining xylanase from Streptomyces olivaceoviridis E-86. To clearly define the stereochemistry at the anomeric carbon during the deglycosylation step, extraneous nucleophiles, such as azide, were adopted to substitute for the missing base catalyst in an appropriate mutant. The X-ray crystallographic visualization provided snapshots of the components of the entire reaction, including the E*S complex, the covalent intermediate, breakdown of the intermediate and the enzyme-product (E*P)complex.
Related Citations:
Crystal structure of Streptomyces olivaceoviridis E-86 beta-xylanase containing xylan-binding domain Fujimoto, Z., Kuno, A., Kaneko, S., Yoshida, S., Kobayashi, H., Kusakabe, I., Mizuno, H. (2000) J Mol Biol 300: 575
Crystal structures of the sugar complexes of Streptomyces olivaceoviridis E-86 xylanase: sugar binding structure of the family 13 carbohydrate binding module Fujimoto, Z., Kuno, A., Kaneko, S., Kobayashi, H., Kusakabe, I., Mizuno, H. (2002) J Mol Biol 316: 65
Crystal structures of decorated xylooligosaccharides bound to a family 10 xylanase from Streptomyces olivaceoviridis E-86 Fujimoto, Z., Kaneko, S., Kuno, A., Kobayashi, H., Kusakabe, I., Mizuno, H. (2004) J Biol Chem 279: 9606
PCR Cloning and Expression of the F/10 Family Xylanse Gene from Streptomyces olivaceoviridis E-86 Kuno, A., Shimizu, D., Kaneko, S., Koyama, Y., Yoshida, S., Kobayashi, H., Hayashi, K., Taira, K., Kusakabe, I. (1998) J Ferment Bioeng 86: 434
Significant enhancement in the binding of p-nitrophenyl-beta-D-xylobioside by the E128H mutant F/10 xylanase from Streptomyces olivaceoviridis E-86 Kuno, A., Shimizu, D., Kaneko, S., Hasegawa, T., Gama, Y., Hayashi, K., Kusakabe, I., Taira, K. (1999) FEBS Lett 450: 299
Organizational Affiliation:
Department of Material and Biological Chemistry, Yamagata University, Japan.
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