Beijerinckia indica beta-fructosyltransferase variant H395R/F473Y in complex with fructose

Experimental Data Snapshot

  • Resolution: 1.36 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

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Characterization and alteration of product specificity of Beijerinckia indica subsp. indica beta-fructosyltransferase.

Li, D.Miyasaka, Y.Kubota, A.Kozono, T.Kitano, Y.Sasaki, N.Fujii, T.Tochio, T.Kadota, Y.Nishikawa, A.Tonozuka, T.

(2023) Biosci Biotechnol Biochem 87: 981-990

  • DOI: https://doi.org/10.1093/bbb/zbad074
  • Primary Citation of Related Structures:  
    8I2Q, 8I2R

  • PubMed Abstract: 

    The trisaccharide 1-kestose, a major constituent of fructooligosaccharide, has strong prebiotic effects. We used high-performance liquid chromatography and 1H nuclear magnetic resonance spectroscopy to show that BiBftA, a β-fructosyltransferase belonging to glycoside hydrolase family 68, from Beijerinckia indica subsp. indica catalyzes transfructosylation of sucrose to produce mostly 1-kestose and levan polysaccharides. We substituted His395 and Phe473 in BiBftA with Arg and Tyr, respectively, and analyzed the reactions of the mutant enzymes with 180 g/L sucrose. The ratio of the molar concentrations of glucose and 1-kestose in the reaction mixture with wild-type BiBftA was 100:8.1, whereas that in the reaction mixture with the variant H395R/F473Y was 100:45.5, indicating that H395R/F473Y predominantly accumulated 1-kestose from sucrose. The X-ray crystal structure of H395R/F473Y suggests that its catalytic pocket is unfavorable for binding of sucrose while favorable for transfructosylation.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-fructosyltransferase523Beijerinckia indica subsp. indicaMutation(s): 0 
Find proteins for B2IF78 (Beijerinckia indica subsp. indica (strain ATCC 9039 / DSM 1715 / NCIMB 8712))
Explore B2IF78 
Go to UniProtKB:  B2IF78
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2IF78
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.36 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.542α = 90
b = 81.697β = 90
c = 99.602γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

  • Released Date: 2023-06-14 
  • Deposition Author(s): Tonozuka, T.

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan20K05956

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 1.1: 2023-06-21
    Changes: Database references
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references