Crystal structure of Streptococcus mutans dextran glucosidase

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 

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Substrate recognition mechanism of alpha-1,6-glucosidic linkage hydrolyzing enzyme, dextran glucosidase from Streptococcus mutans.

Hondoh, H.Saburi, W.Mori, H.Okuyama, M.Nakada, T.Matsuura, Y.Kimura, A.

(2008) J Mol Biol 378: 911-920

  • DOI: https://doi.org/10.1016/j.jmb.2008.03.016
  • Primary Citation of Related Structures:  
    2ZIC, 2ZID

  • PubMed Abstract: 

    We have determined the crystal structure of Streptococcus mutans dextran glucosidase, which hydrolyzes the alpha-1,6-glucosidic linkage of isomaltooligosaccharides from their non-reducing ends to produce alpha-glucose. By using the mutant of catalytic acid Glu236-->Gln, its complex structure with the isomaltotriose, a natural substrate of this enzyme, has been determined. The enzyme has 536 amino acid residues and a molecular mass of 62,001 Da. The native and the complex structures were determined by the molecular replacement method and refined to 2.2 A resolution, resulting in a final R-factor of 18.3% for significant reflections in the native structure and 18.4% in the complex structure. The enzyme is composed of three domains, A, B and C, and has a (beta/alpha)(8)-barrel in domain A, which is common to the alpha-amylase family enzymes. Three catalytic residues are located at the bottom of the active site pocket and the bound isomaltotriose occupies subsites -1 to +2. The environment of the glucose residue at subsite -1 is similar to the environment of this residue in the alpha-amylase family. Hydrogen bonds between Asp60 and Arg398 and O4 atom of the glucose unit at subsite -1 accomplish recognition of the non-reducing end of the bound substrate. The side-chain atoms of Glu371 and Lys275 form hydrogen bonds with the O2 and O3 atoms of the glucose residue at subsite +1. The positions of atoms that compose the scissile alpha-1,6-glucosidic linkage (C1, O6 and C6 atoms) are identical with the positions of the atoms in the scissile alpha-1,4 linkage (C1, O4 and C4 atoms) of maltopentaose in the alpha-amylase structure from Bacillus subtilis. The comparison with the alpha-amylase suggests that Val195 of the dextran glucosidase and the corresponding residues of alpha-1,6-hydrolyzing enzymes participate in the determination of the substrate specificity of these enzymes.

  • Organizational Affiliation

    Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan. hondoh@abs.agr.hokudai.ac.jp

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dextran glucosidase543Streptococcus mutansMutation(s): 1 
Gene Names: dexB
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: 2.20 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.72α = 90
b = 86.47β = 90
c = 104.3γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-11-01
    Changes: Data collection, Refinement description