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Hokkaido University Collection of Scholarly and Academic Papers >
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Structural Elucidation of Dextran Degradation Mechanism by Streptococcus mutans Dextranase Belonging to Glycoside Hydrolase Family 66
| Title: | Structural Elucidation of Dextran Degradation Mechanism by Streptococcus mutans Dextranase Belonging to Glycoside Hydrolase Family 66 |
| Authors: | Suzuki, Nobuhiro Browse this author | | Kim, Young-Min Browse this author | | Fujimoto, Zui Browse this author | | Momma, Mitsuru Browse this author | | Okuyama, Masayuki Browse this author →KAKEN DB | | Mori, Haruhide Browse this author →KAKEN DB | | Funane, Kazumi Browse this author | | Kimura, Atsuo Browse this author →KAKEN DB |
| Keywords: | dextranase | | crystal structure | | catalytic mechanism |
| Issue Date: | 8-Jun-2012 |
| Publisher: | American Society for Biochemistry and Molecular Biology |
| Journal Title: | Journal of Biological Chemistry |
| Volume: | 287 |
| Issue: | 24 |
| Start Page: | 19916 |
| End Page: | 19926 |
| Publisher DOI: | 10.1074/jbc.M112.342444 |
| Abstract: | 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. |
| Rights: | 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. |
| Type: | article (author version) |
| URI: | http://hdl.handle.net/2115/51763 |
| Appears in Collections: | 農学院・農学研究院 (Graduate School of Agriculture / Faculty of Agriculture) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)
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Submitter: 木村 淳夫
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