Structure of D188A-fructofuranosidase from Rhodotorula dairenesis in complex with sucrose

Experimental Data Snapshot

  • Resolution: 2.38 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

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Insights into the Structure of the Highly Glycosylated Ffase from Rhodotorula dairenensis Enhance Its Biotechnological Potential.

Jimenez-Ortega, E.Narmontaite, E.Gonzalez-Perez, B.Plou, F.J.Fernandez-Lobato, M.Sanz-Aparicio, J.

(2022) Int J Mol Sci 23

  • DOI: https://doi.org/10.3390/ijms232314981
  • Primary Citation of Related Structures:  
    8BEQ, 8BES, 8BET, 8BEU

  • PubMed Abstract: 

    Rhodotorula dairenensis β-fructofuranosidase is a highly glycosylated enzyme with broad substrate specificity that catalyzes the synthesis of 6-kestose and a mixture of the three series of fructooligosaccharides (FOS), fructosylating a variety of carbohydrates and other molecules as alditols. We report here its three-dimensional structure, showing the expected bimodular arrangement and also a unique long elongation at its N-terminus containing extensive O-glycosylation sites that form a peculiar arrangement with a protruding loop within the dimer. This region is not required for activity but could provide a molecular tool to target the dimeric protein to its receptor cellular compartment in the yeast. A truncated inactivated form was used to obtain complexes with fructose, sucrose and raffinose, and a Bis-Tris molecule was trapped, mimicking a putative acceptor substrate. The crystal structure of the complexes reveals the major traits of the active site, with Asn387 controlling the substrate binding mode. Relevant residues were selected for mutagenesis, the variants being biochemically characterized through their hydrolytic and transfructosylating activity. All changes decrease the hydrolytic efficiency against sucrose, proving their key role in the activity. Moreover, some of the generated variants exhibit redesigned transfructosylating specificity, which may be used for biotechnological purposes to produce novel fructosyl-derivatives.

  • Organizational Affiliation

    Department of Crystallography and Structural Biology, Institute of Physical-Chemistry Rocasolano, CSIC, 28006 Madrid, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
675Rhodotorula dairenensisMutation(s): 1 
Gene Names: INV
Find proteins for A0A856TAI5 (Rhodotorula dairenensis)
Explore A0A856TAI5 
Go to UniProtKB:  A0A856TAI5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A856TAI5
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
E, H, K
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
F, I, J
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G56014GC
GlyCosmos:  G56014GC
GlyGen:  G56014GC
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
L, M, N, O
Glycosylation Resources
GlyTouCan:  G05551OP
GlyCosmos:  G05551OP
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth D]
BB [auth D]
CB [auth D]
DA [auth B]
EA [auth B]
AB [auth D],
BB [auth D],
CB [auth D],
DA [auth B],
EA [auth B],
FA [auth B],
GA [auth B],
HA [auth B],
IA [auth B],
JA [auth B],
OA [auth C],
PA [auth C],
QA [auth C],
RA [auth C],
SA [auth C],
T [auth A],
TA [auth C],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
XA [auth D],
Y [auth A],
YA [auth D],
Z [auth A],
ZA [auth D]
C8 H15 N O6
Query on MAN

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
KA [auth C]
LA [auth C]
AA [auth B],
BA [auth B],
CA [auth B],
KA [auth C],
LA [auth C],
MA [auth C],
NA [auth C],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
UA [auth D],
VA [auth D],
WA [auth D]
C6 H12 O6
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Resolution: 2.38 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.343α = 90
b = 112.813β = 104.74
c = 139.083γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpain--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-28
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description