8I2R

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-fructosyltransferase523Beijerinckia indica subsp. indicaMutation(s): 0 
EC: 2.4.1.100
UniProt
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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



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