Structure of E230A-fructofuranosidase from Schwanniomyces occidentalis complexed with fructosylnystose

Experimental Data Snapshot

  • Resolution: 2.68 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 2.1 of the entry. See complete history


Structural and kinetic insights reveal that the amino acid pair GLN228/ASN254 modulates the transfructosylating specificity of Schwanniomyces occidentalis beta-fructofuranosidase, an enzyme that produces prebiotics.

Sainz-Polo, M.A.Gonzalez-Perez, D.Gonzalez, B.Plou, F.J.Fernandez-Lobato, M.Sanz-Aparicio, J.

(2012) J Biol Chem 287: 19674-19686

  • DOI: https://doi.org/10.1074/jbc.M112.355503
  • Primary Citation of Related Structures:  
    3U14, 3U75

  • PubMed Abstract: 

    Schwanniomyces occidentalis β-fructofuranosidase (Ffase) is a GH32 dimeric enzyme that releases fructose from the nonreducing end of various oligosaccharides and essential storage fructans such as inulin. It also catalyzes the transfer of a fructosyl unit to an acceptor producing 6-kestose and 1-kestose, prebiotics that stimulate the growth of bacteria beneficial for human health. We report here the crystal structure of inactivated Ffase complexed with fructosylnystose and inulin, which shows the intricate net of interactions keeping the substrate tightly bound at the active site. Up to five subsites were observed, the sugar unit located at subsite +3 being recognized by interaction with the β-sandwich domain of the adjacent subunit within the dimer. This explains the high activity observed against long substrates, giving the first experimental evidence of the direct role of a GH32 β-sandwich domain in substrate binding. Crucial residues were mutated and their hydrolase/transferase (H/T) activities were fully characterized, showing the involvement of the Gln-228/Asn-254 pair in modulating the H/T ratio and the type β(2-1)/β(2-6) linkage formation. We generated Ffase mutants with new transferase activity; among them, Q228V gives almost specifically 6-kestose, whereas N254T produces a broader spectrum product including also neokestose. A model for the mechanism of the Ffase transfructosylation reaction is proposed. The results contribute to an understanding of the molecular basis regulating specificity among GH-J clan members, which represent an interesting target for rational design of enzymes, showing redesigned activities to produce tailor-made fructooligosaccharides.

  • Organizational Affiliation

    Centro de Biología Molecular Severo Ochoa, Departamento de Biología Molecular, Universidad Autónoma de Madrid-Consejo Superior de Investigaciones, Cantoblanco, 28049 Madrid, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
535Schwanniomyces occidentalisMutation(s): 0 
Find proteins for E5D0X5 (Schwanniomyces occidentalis)
Explore E5D0X5 
Go to UniProtKB:  E5D0X5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE5D0X5
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
E, F, G, H
Glycosylation Resources
GlyTouCan:  G14615XY
GlyCosmos:  G14615XY
Experimental Data & Validation

Experimental Data

  • Resolution: 2.68 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.245 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.207α = 89.91
b = 92.663β = 82.96
c = 117.753γ = 85.82
Software Package:
Software NamePurpose
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-25
    Type: Initial release
  • Version 1.1: 2012-05-02
    Changes: Database references
  • Version 1.2: 2013-07-10
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary