Flavobacterium johnsoniae GH31 dextranase, FjDex31A, complexed with glucose

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report

This is version 2.1 of the entry. See complete history


Structural insights into polysaccharide recognition by Flavobacterium johnsoniae dextranase, a member of glycoside hydrolase family 31.

Tsutsumi, K.Gozu, Y.Nishikawa, A.Tonozuka, T.

(2020) FEBS J 287: 1195-1207

  • DOI: https://doi.org/10.1111/febs.15074
  • Primary Citation of Related Structures:  
    6JR6, 6JR7, 6JR8

  • PubMed Abstract: 

    Glycoside hydrolase family (GH) 31 contains a large variety of enzymes, but the major members are enzymes that act on relatively small oligosaccharides such as α-glucosidase. Here, we determined the crystal structure of Flavobacterium johnsoniae dextranase (FjDex31A), an enzyme from F. johnsoniae that hydrolyzes a polysaccharide, dextran. FjDex31A is composed of four domains: an N-terminal domain, a catalytic domain, a proximal C-terminal domain, and a distal C-terminal domain, as observed in typical GH31 enzymes. However, the architecture of active site residues in FjDex31A, other than subsite -1, is markedly different from that of other GH31 enzymes. The FjDex31A structure in complex with isomaltotriose shows that Gly273 and Tyr524, both of which interact with an α-glucose residue at subsite -2, as well as Trp376 and Leu308-cisGln309, are especially unique to FjDex31A. Site-directed mutagenesis of Gly273 and Tyr524 resulted in a decrease in the hydrolysis of polysaccharides dextran and pullulan, as well as that of the disaccharide isomaltose. These results suggest that, regardless of the length of sugar chains of the substrates, binding of FjDex31A to the substrates at subsite -2 is likely to be important for its activity. DATABASE: Structural data are available in the Protein Data Bank under the accession numbers 6JR6, 6JR7, and 6JR8.

  • Organizational Affiliation

    Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Candidate alpha-glycosidase Glycoside hydrolase family 31
A, B, C, D
838Flavobacterium johnsoniae UW101Mutation(s): 0 
Gene Names: Fjoh_4430
Find proteins for A5FBI1 (Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / JCM 8514 / NBRC 14942 / NCIMB 11054 / UW101))
Explore A5FBI1 
Go to UniProtKB:  A5FBI1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5FBI1
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
E, F, G, H
Glycosylation Resources
GlyTouCan:  G69864PN
GlyCosmos:  G69864PN
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MPD

Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
M [auth B]
N [auth B]
P [auth C]
J [auth A],
K [auth A],
M [auth B],
N [auth B],
P [auth C],
Q [auth C],
T [auth D],
U [auth D]
C6 H14 O2
Query on ACT

Download Ideal Coordinates CCD File 
I [auth A],
L [auth B],
O [auth C],
R [auth D],
S [auth D]
C2 H3 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.591α = 87.05
b = 102.602β = 113.07
c = 114.13γ = 118.53
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

  • Released Date: 2019-04-24 
  • Deposition Author(s): Tonozuka, T.

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan16K07687

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-10-09
    Changes: Data collection, Database references
  • Version 1.2: 2020-04-01
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary