Arthrobacter globiformis T6 isomalto-dextranse

Experimental Data Snapshot

  • Resolution: 1.44 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 

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This is version 1.4 of the entry. See complete history


Crystal Structure and Mutational Analysis of Isomalto-dextranase, a Member of Glycoside Hydrolase Family 27

Okazawa, Y.Miyazaki, T.Yokoi, G.Ishizaki, Y.Nishikawa, A.Tonozuka, T.

(2015) J Biol Chem 290: 26339-26349

  • DOI: https://doi.org/10.1074/jbc.M115.680942
  • Primary Citation of Related Structures:  
    5AWO, 5AWP, 5AWQ

  • PubMed Abstract: 

    Arthrobacter globiformis T6 isomalto-dextranase (AgIMD) is an enzyme that liberates isomaltose from the non-reducing end of a polymer of glucose, dextran. AgIMD is classified as a member of the glycoside hydrolase family (GH) 27, which comprises mainly α-galactosidases and α-N-acetylgalactosaminidases, whereas AgIMD does not show α-galactosidase or α-N-acetylgalactosaminidase activities. Here, we determined the crystal structure of AgIMD. AgIMD consists of the following three domains: A, C, and D. Domains A and C are identified as a (β/α)8-barrel catalytic domain and an antiparallel β-structure, respectively, both of which are commonly found in GH27 enzymes. However, domain A of AgIMD has subdomain B, loop-1, and loop-2, all of which are not found in GH27 human α-galactosidase. AgIMD in a complex with trisaccharide panose shows that Asp-207, a residue in loop-1, is involved in subsite +1. Kinetic parameters of the wild-type and mutant enzymes for the small synthetic saccharide p-nitrophenyl α-isomaltoside and the polysaccharide dextran were compared, showing that Asp-207 is important for the catalysis of dextran. Domain D is classified as carbohydrate-binding module (CBM) 35, and an isomaltose molecule is seen in this domain in the AgIMD-isomaltose complex. Domain D is highly homologous to CBM35 domains found in GH31 and GH66 enzymes. The results here indicate that some features found in GH13, -31, and -66 enzymes, such as subdomain B, residues at the subsite +1, and the CBM35 domain, are also observed in the GH27 enzyme AgIMD and thus provide insights into the evolutionary relationships among GH13, -27, -31, -36, and -66 enzymes.

  • Organizational Affiliation

    From the Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isomaltodextranase610Arthrobacter globiformisMutation(s): 0 
Gene Names: g2d
Find proteins for Q7WSN5 (Arthrobacter globiformis)
Explore Q7WSN5 
Go to UniProtKB:  Q7WSN5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7WSN5
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on SME
Experimental Data & Validation

Experimental Data

  • Resolution: 1.44 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.6α = 90
b = 123.6β = 90
c = 84.72γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

  • Released Date: 2015-09-09 
  • Deposition Author(s): Tonozuka, T.

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 1.1: 2015-10-21
    Changes: Database references
  • Version 1.2: 2015-11-04
    Changes: Structure summary
  • Version 1.3: 2015-11-11
    Changes: Database references
  • Version 1.4: 2020-02-26
    Changes: Data collection, Database references, Derived calculations