open access

https://hdl.handle.net/2115/51763

Structural Elucidation of Dextran Degradation Mechanism by Streptococcus mutans Dextranase Belonging to Glycoside Hydrolase Family 66

英語

catalytic mechanism

2012-06-08

American Society for Biochemistry and Molecular Biology

Journal of Biological Chemistry

287(24)

19916-19926

Dextranase is an enzyme that hydrolyzes dextran α-1,6 linkages. Streptococcus mutans dextranase (SmDex) belongs to glycoside hydrolase family 66, producing isomaltooligosaccharides of various sizes, and consisting of at least five amino acid sequence regions. The crystal structure of the conserved fragment from Gln-100 to Ile-732 of SmDex, devoid of its N and C-terminal variable regions, was determined at 1.6 Å resolution and found to contain three structural domains. Domain N possessed an immunoglobulin-like β-sandwich fold, domain A the enzyme's catalytic module, comprising a (β/α)8-barrel, and domain C formed a β-sandwich structure containing two Greek key motifs. Two ligand complex structures were also determined and, in the enzyme/isomaltotriose complex structure, the bound isomaltooligosaccharide with four glucose moieties was observed in the catalytic glycone cleft and considered to be the transglycosylation product of the enzyme, indicating the presence of four subsites -4 to -1 in the catalytic cleft. The complexed structure with 4',5'-epoxypentyl-α-D-glucopyranoside, a suicide substrate of the enzyme, revealed that the epoxide ring reacted to form a covalent bond with the Asp-385 sidechain. These structures collectively indicated that Asp-385 was the catalytic nucleophile and Glu-453 the acid/base of the double displacement mechanism, in which the enzyme showed a retaining catalytic character. This is the first structural report for a GH-66 enzyme elucidating the enzyme's catalytic machinery.

学術雑誌論文

Accepted Manuscript

This research was originally published in Journal of Biological Chemistry. Nobuhiro Suzuki; Young-Min Kim; Zui Fujimoto; Mitsuru Momma; Masayuki Okuyama; Haruhide Mori; Kazumi Funane; Atsuo Kimura. Structural Elucidation of Dextran Degradation Mechanism by Streptococcus mutans Dextranase Belonging to Glycoside Hydrolase Family 66. Journal of Biological Chemistry. 2012; 287:19916-19926. © the American Society for Biochemistry and Molecular Biology.

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