5XHA | pdb_00005xha

Aspergillus kawachii beta-fructofuranosidase complexed with fructose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.210 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

Crystal structure of a beta-fructofuranosidase with high transfructosylation activity from Aspergillus kawachii

Nagaya, M.Kimura, M.Gozu, Y.Sato, S.Hirano, K.Tochio, T.Nishikawa, A.Tonozuka, T.

(2017) Biosci Biotechnol Biochem 81: 1786-1795

  • DOI: https://doi.org/10.1080/09168451.2017.1353405
  • Primary Citation Related Structures: 
    5XH8, 5XH9, 5XHA

  • PubMed Abstract: 

    β-Fructofuranosidases belonging to glycoside hydrolase family (GH) 32 are enzymes that hydrolyze sucrose. Some GH32 enzymes also catalyze transfructosylation to produce fructooligosaccharides. We found that Aspergillus kawachii IFO 4308 β-fructofuranosidase (AkFFase) produces fructooligosaccharides, mainly 1-kestose, from sucrose. We determined the crystal structure of AkFFase. AkFFase is composed of an N-terminal small component, a β-propeller catalytic domain, an α-helical linker, and a C-terminal β-sandwich, similar to other GH32 enzymes. AkFFase forms a dimer, and the dimerization pattern is different from those of other oligomeric GH32 enzymes. The complex structure of AkFFase with fructose unexpectedly showed that fructose binds both subsites -1 and +1, despite the fact that the catalytic residues were not mutated. Fructose at subsite +1 interacts with Ile146 and Glu296 of AkFFase via direct hydrogen bonds.


  • Organizational Affiliation
    • a Department of Applied Biological Science , Tokyo University of Agriculture and Technology , Fuchu , Japan.

Macromolecule Content 

  • Total Structure Weight: 66.54 kDa 
  • Atom Count: 5,012 
  • Modeled Residue Count: 605 
  • Deposited Residue Count: 605 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Extracellular invertase605Aspergillus luchuensis IFO 4308Mutation(s): 0 
Gene Names: AKAW_06215

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-fructofuranose-(2-1)-beta-D-fructofuranose
B
2N/A
Glycosylation Resources
GlyTouCan: G99327ZM
GlyCosmos: G99327ZM

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.210 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.357α = 90
b = 108.357β = 90
c = 152.852γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-19
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Database references
  • Version 1.2: 2017-08-16
    Changes: 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