Structural insights into the catalytic reaction that is involved in the reorientation of Trp238 at the substrate-binding site in GH13 dextran glucosidase

Momoko Kobayashi, Wataru Saburi, Daichi Nakatsuka, Hironori Hondoh, Koji Kato, Masayuki Okuyama, Haruhide Mori, Atsuo Kimura, Min Yao

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)484-489
Number of pages6
JournalFEBS Letters
Volume589
Issue number4
DOIs
Publication statusPublished - Feb 13 2015
Externally publishedYes

Fingerprint

exo-1,6-alpha-glucosidase
Streptococcus mutans
Binding Sites
Substrates
Nucleophiles
Glycoside Hydrolases
Conformations
Hydrolysis
Crystal structure
Kinetics
Acids
Enzymes

Keywords

  • Acceptor specificity
  • Dextran glucosidase
  • Glucosyl-enzyme intermediate transglucosylation
  • Glycoside hydrolase family 13
  • Retaining glycosidase

ASJC Scopus subject areas

  • Structural Biology
  • Biophysics
  • Biochemistry
  • Molecular Biology
  • Genetics
  • Cell Biology

Cite this

Structural insights into the catalytic reaction that is involved in the reorientation of Trp238 at the substrate-binding site in GH13 dextran glucosidase. / Kobayashi, Momoko; Saburi, Wataru; Nakatsuka, Daichi; Hondoh, Hironori; Kato, Koji; Okuyama, Masayuki; Mori, Haruhide; Kimura, Atsuo; Yao, Min.

In: FEBS Letters, Vol. 589, No. 4, 13.02.2015, p. 484-489.

Research output: Contribution to journalArticle

Kobayashi, Momoko ; Saburi, Wataru ; Nakatsuka, Daichi ; Hondoh, Hironori ; Kato, Koji ; Okuyama, Masayuki ; Mori, Haruhide ; Kimura, Atsuo ; Yao, Min. / Structural insights into the catalytic reaction that is involved in the reorientation of Trp238 at the substrate-binding site in GH13 dextran glucosidase. In: FEBS Letters. 2015 ; Vol. 589, No. 4. pp. 484-489.
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AU - Saburi, Wataru

AU - Nakatsuka, Daichi

AU - Hondoh, Hironori

AU - Kato, Koji

AU - Okuyama, Masayuki

AU - Mori, Haruhide

AU - Kimura, Atsuo

AU - Yao, Min

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