Structure of dextran glucosidase with glucose

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

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This is version 1.3 of the entry. See complete history


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

Kobayashi, M.Saburi, W.Nakatsuka, D.Hondoh, H.Kato, K.Okuyama, M.Mori, H.Kimura, A.Yao, M.

(2015) FEBS Lett 589: 484-489

  • DOI: https://doi.org/10.1016/j.febslet.2015.01.005
  • Primary Citation of Related Structures:  
    4WLC, 4XB3

  • PubMed 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 2.4Å 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.

  • Organizational Affiliation

    Graduate School of Life Science, Hokkaido University, Kita-10, Nishi-8, Kita-ku, Sapporo 060-0810, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glucan 1,6-alpha-glucosidase536Streptococcus mutans UA159Mutation(s): 2 
Gene Names: dexBSMU_883
Find proteins for Q99040 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159))
Explore Q99040 
Go to UniProtKB:  Q99040
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99040
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.989α = 90
b = 83.736β = 90
c = 103.79γ = 90
Software Package:
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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
the Japan Society for the Promotion of ScienceJapan24-871
the Ministry of Education, Culture, Sports, Science and Technology, JapanJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-26
    Type: Initial release
  • Version 1.1: 2020-02-05
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary