Crystal structure of GH65 alpha-1,2-glucosidase from Flavobacterium johnsoniae

Experimental Data Snapshot

  • Resolution: 1.54 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.171 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


Structure of a bacterial alpha-1,2-glucosidase defines mechanisms of hydrolysis and substrate specificity in GH65 family hydrolases.

Nakamura, S.Nihira, T.Kurata, R.Nakai, H.Funane, K.Park, E.Y.Miyazaki, T.

(2021) J Biol Chem 297: 101366-101366

  • DOI: https://doi.org/10.1016/j.jbc.2021.101366
  • Primary Citation of Related Structures:  
    7FE3, 7FE4

  • PubMed Abstract: 

    Glycoside hydrolase family 65 (GH65) comprises glycoside hydrolases (GHs) and glycoside phosphorylases (GPs) that act on α-glucosidic linkages in oligosaccharides. All previously reported bacterial GH65 enzymes are GPs, whereas all eukaryotic GH65 enzymes known are GHs. In addition, to date, no crystal structure of a GH65 GH has yet been reported. In this study, we use biochemical experiments and X-ray crystallography to examine the function and structure of a GH65 enzyme from Flavobacterium johnsoniae (FjGH65A) that shows low amino acid sequence homology to reported GH65 enzymes. We found that FjGH65A does not exhibit phosphorolytic activity, but it does hydrolyze kojibiose (α-1,2-glucobiose) and oligosaccharides containing a kojibiosyl moiety without requiring inorganic phosphate. In addition, stereochemical analysis demonstrated that FjGH65A catalyzes this hydrolytic reaction via an anomer-inverting mechanism. The three-dimensional structures of FjGH65A in native form and in complex with glucose were determined at resolutions of 1.54 and 1.40 Å resolutions, respectively. The overall structure of FjGH65A resembled those of other GH65 GPs, and the general acid catalyst Glu 472 was conserved. However, the amino acid sequence forming the phosphate-binding site typical of GH65 GPs was not conserved in FjGH65A. Moreover, FjGH65A had the general base catalyst Glu 616 instead, which is required to activate a nucleophilic water molecule. These results indicate that FjGH65A is an α-1,2-glucosidase and is the first bacterial GH found in the GH65 family.

  • Organizational Affiliation

    Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Candidate alpha glycoside phosphorylase Glycoside hydrolase family 65
A, B, C
678Flavobacterium johnsoniae UW101Mutation(s): 0 
Gene Names: Fjoh_4428
Find proteins for A5FBJ5 (Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / JCM 8514 / NBRC 14942 / NCIMB 11054 / UW101))
Explore A5FBJ5 
Go to UniProtKB:  A5FBJ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5FBJ5
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
D [auth A]
E [auth A]
AA [auth C],
BA [auth C],
CA [auth C],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.54 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.171 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.83α = 90
b = 193.97β = 116.601
c = 111.735γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
Cootmodel building

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan19K15748

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-10
    Type: Initial release
  • Version 1.1: 2021-12-08
    Changes: Database references