TY - JOUR
T1 - Structural insights into the catalytic reaction that is involved in the reorientation of Trp238 at the substrate-binding site in GH13 dextran glucosidase
AU - Kobayashi, Momoko
AU - Saburi, Wataru
AU - Nakatsuka, Daichi
AU - Hondoh, Hironori
AU - Kato, Koji
AU - Okuyama, Masayuki
AU - Mori, Haruhide
AU - Kimura, Atsuo
AU - Yao, Min
N1 - Funding Information:
We thank the staffs of beamline BL-38B1 at SPring-8 and beamline BL-17A at Photon Factory. A part of this work was supported by Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science (Grant Number, 24 871 ) and Platform for Drug Discovery, Informatics, and Structural Life Science from the Ministry of Education, Culture, Sports, Science, and Technology , Japan.
Publisher Copyright:
© 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
PY - 2015/2/13
Y1 - 2015/2/13
N2 - Streptococcus mutans dextran glucosidase (SmDG) belongs to glycoside hydrolase family 13, and catalyzes both the hydrolysis of substrates such as isomaltooligosaccharides and subsequent transglucosylation to form α-(1 → 6)-glucosidic linkage at the substrate non-reducing ends. Here, we report the 2.4 Å resolution crystal structure of glucosyl-enzyme intermediate of SmDG. In the obtained structure, the Trp238 side-chain that constitutes the substrate-binding site turned away from the active pocket, concurrently with conformational changes of the nucleophile and the acid/base residues. Different conformations of Trp238 in each reaction stage indicated its flexibility. Considering the results of kinetic analyses, such flexibility may reflect a requirement for the reaction mechanism of SmDG.
AB - Streptococcus mutans dextran glucosidase (SmDG) belongs to glycoside hydrolase family 13, and catalyzes both the hydrolysis of substrates such as isomaltooligosaccharides and subsequent transglucosylation to form α-(1 → 6)-glucosidic linkage at the substrate non-reducing ends. Here, we report the 2.4 Å resolution crystal structure of glucosyl-enzyme intermediate of SmDG. In the obtained structure, the Trp238 side-chain that constitutes the substrate-binding site turned away from the active pocket, concurrently with conformational changes of the nucleophile and the acid/base residues. Different conformations of Trp238 in each reaction stage indicated its flexibility. Considering the results of kinetic analyses, such flexibility may reflect a requirement for the reaction mechanism of SmDG.
KW - Acceptor specificity
KW - Dextran glucosidase
KW - Glucosyl-enzyme intermediate transglucosylation
KW - Glycoside hydrolase family 13
KW - Retaining glycosidase
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U2 - 10.1016/j.febslet.2015.01.005
DO - 10.1016/j.febslet.2015.01.005
M3 - Article
C2 - 25595454
AN - SCOPUS:84964300513
SN - 0014-5793
VL - 589
SP - 484
EP - 489
JO - FEBS Letters
JF - FEBS Letters
IS - 4
ER -