3U75

Structure of E230A-fructofuranosidase from Schwanniomyces occidentalis complexed with fructosylnystose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.241 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1074/jbc.M112.355503
  • Primary Citation of Related Structures:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fructofuranosidase
A, B, C, D
535Schwanniomyces occidentalisMutation(s): 0 
EC: 3.2.1.26
Find proteins for E5D0X5 (Schwanniomyces occidentalis)
Go to UniProtKB:  E5D0X5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FRU
Query on FRU

Download SDF File 
Download CCD File 
A, B, C, D
FRUCTOSE
C6 H12 O6
RFSUNEUAIZKAJO-ARQDHWQXSA-N
 Ligand Interaction
GLC
Query on GLC

Download SDF File 
Download CCD File 
A, B, C, D
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.241 
  • 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
MOSFLMdata reduction
REFMACrefinement
MOLREPphasing
ADSCdata collection
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-25
    Type: Initial release
  • Version 1.1: 2012-05-02
    Type: Database references
  • Version 1.2: 2013-07-10
    Type: Database references