6M0D

Beijerinckia indica beta-fructosyltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of a glycoside hydrolase family 68 beta-fructosyltransferase fromBeijerinckia indicasubsp.indicain complex with fructose.

Tonozuka, T.Kitamura, J.Nagaya, M.Kawai, R.Nishikawa, A.Hirano, K.Tamura, K.Fujii, T.Tochio, T.

(2020) Biosci Biotechnol Biochem : 1-13

  • DOI: 10.1080/09168451.2020.1804317
  • Primary Citation of Related Structures:  
    6M0D, 6M0E

  • PubMed Abstract: 
  • An enzyme belonging to glycoside hydrolase family 68 (GH68) from Beijerinckia indica subsp. indica NBRC 3744 was expressed in Escherichia coli . Biochemical characterization showed that the enzyme was identified to be a β-fr ...

    An enzyme belonging to glycoside hydrolase family 68 (GH68) from Beijerinckia indica subsp. indica NBRC 3744 was expressed in Escherichia coli . Biochemical characterization showed that the enzyme was identified to be a β-fructosyltransferase (BiBftA). Crystallization of a full-length BiBftA was initially attempted, but no crystals were obtained. We constructed a variant in which 5 residues (Pro199-Gly203) and 13 residues (Leu522-Gln534) in potentially flexible regions were deleted, and we successfully crystallized this variant BiBftA. BiBftA is composed of a five-bladed β-propeller fold as in other GH68 enzymes. The structure of BiBftA in complex with fructose unexpectedly indicated that one β-fructofuranose (β-Fru f ) molecule and one β-fructopyranose molecule bind to the catalytic pocket. The orientation of β-Fru f at subsite -1 is tilted from the orientation observed in most GH68 enzymes, presenting a second structure of a GH68 enzyme in complex with the tilted binding mode of β-Fru f.


    Organizational Affiliation

    R&D Center, B Food Science Co. Ltd , Aichi, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LevansucraseA523Beijerinckia indica subsp. indica ATCC 9039Mutation(s): 0 
Gene Names: Bind_2021
EC: 2.4.1.10
Find proteins for B2IF78 (Beijerinckia indica subsp. indica (strain ATCC 9039 / DSM 1715 / NCIB 8712))
Explore B2IF78 
Go to UniProtKB:  B2IF78
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.891α = 90
b = 80.9β = 90
c = 92.661γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2020-02-21 
  • Released Date: 2020-08-12 
  • Deposition Author(s): Tonozuka, T.

Revision History 

  • Version 1.0: 2020-08-12
    Type: Initial release
  • Version 1.1: 2020-08-19
    Changes: Database references