Structure of fructofuranosidase from Xanthophyllomyces dendrorhous

Experimental Data Snapshot

  • Resolution: 2.14 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

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Structural Analysis of Beta-Fructofuranosidase from Xanthophyllomyces Dendrorhous Reveals Unique Features and the Crucial Role of N-Glycosylation in Oligomerization and Activity

Ramirez-Escudero, M.Gimeno-Perez, M.Gonzalez, B.Linde, D.Merdzo, Z.Fernandez-Lobato, M.Sanz-Aparicio, J.

(2016) J Biol Chem 291: 6843

  • DOI: https://doi.org/10.1074/jbc.M115.708495
  • Primary Citation of Related Structures:  
    5ANN, 5FIX, 5FK7, 5FK8, 5FKB, 5FKC, 5FMB, 5FMC, 5FMD

  • PubMed Abstract: 

    Xanthophyllomyces dendrorhousβ-fructofuranosidase (XdINV)is a highly glycosylated dimeric enzyme that hydrolyzes sucrose and releases fructose from various fructooligosaccharides (FOS) and fructans. It also catalyzes the synthesis of FOS, prebiotics that stimulate the growth of beneficial bacteria in human gut. In contrast to most fructosylating enzymes, XdINV produces neo-FOS, which makes it an interesting biotechnology target. We present here its three-dimensional structure, which shows the expected bimodular arrangement and also a long extension of its C terminus that together with anN-linked glycan mediate the formation of an unusual dimer. The two active sites of the dimer are connected by a long crevice, which might indicate its potential ability to accommodate branched fructans. This arrangement could be representative of a group of GH32 yeast enzymes having the traits observed in XdINV. The inactive D80A mutant was used to obtain complexes with relevant substrates and products, with their crystals structures showing at least four binding subsites at each active site. Moreover, two different positions are observed from subsite +2 depending on the substrate, and thus, a flexible loop (Glu-334-His-343) is essential in binding sucrose and β(2-1)-linked oligosaccharides. Conversely, β(2-6) and neo-type substrates are accommodated mainly by stacking to Trp-105, explaining the production of neokestose and the efficient fructosylating activity of XdINV on α-glucosides. The role of relevant residues has been investigated by mutagenesis and kinetics measurements, and a model for the transfructosylating reaction has been proposed. The plasticity of its active site makes XdINV a valuable and flexible biocatalyst to produce novel bioconjugates.

  • Organizational Affiliation

    From the Department of Crystallography and Structural Biology, Institute of Physical-Chemistry "Rocasolano," Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid and.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
665Phaffia rhodozymaMutation(s): 0 
Find proteins for J7HDY4 (Phaffia rhodozyma)
Explore J7HDY4 
Go to UniProtKB:  J7HDY4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ7HDY4
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
C, F
Glycosylation Resources
GlyTouCan:  G09724ZC
GlyCosmos:  G09724ZC
GlyGen:  G09724ZC
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
D, G
Glycosylation Resources
GlyTouCan:  G40702WU
GlyCosmos:  G40702WU
GlyGen:  G40702WU
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
E, H
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
EA [auth B]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
FA [auth B],
GA [auth B],
HA [auth B],
IA [auth B],
J [auth A],
JA [auth B],
K [auth A],
KA [auth B],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A]
C8 H15 N O6
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A],
LA [auth B],
Y [auth A],
Z [auth B]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.14 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.62α = 90
b = 205.18β = 90
c = 145.77γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-10
    Type: Initial release
  • Version 1.1: 2016-04-06
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description, Structure summary