3KF3

Structure of fructofuranosidase from Schwanniomyces occidentalis complexed with fructose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and kinetic analysis of Schwanniomyces occidentalis invertase reveals a new oligomerization pattern and the role of its supplementary domain in substrate binding

Alvaro-Benito, M.Polo, A.Gonzalez, B.Fernandez-Lobato, M.Sanz-Aparicio, J.

(2010) J.Biol.Chem. 285: 13930-13941

  • DOI: 10.1074/jbc.M109.095430
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Schwanniomyces occidentalis invertase is an extracellular enzyme that hydrolyzes sucrose and releases beta-fructose from various oligosaccharides and essential storage fructan polymers such as inulin. We report here the three-dimensional structure of ...

    Schwanniomyces occidentalis invertase is an extracellular enzyme that hydrolyzes sucrose and releases beta-fructose from various oligosaccharides and essential storage fructan polymers such as inulin. We report here the three-dimensional structure of Sw. occidentalis invertase at 2.9 A resolution and its complex with fructose at 1.9 A resolution. The monomer presents a bimodular arrangement common to other GH32 enzymes, with an N-terminal 5-fold beta-propeller catalytic domain and a C-terminal beta-sandwich domain for which the function has been unknown until now. However, the dimeric nature of Sw. occidentalis invertase reveals a unique active site cleft shaped by both subunits that may be representative of other yeast enzymes reported to be multimeric. Binding of the tetrasaccharide nystose and the polymer inulin was explored by docking analysis, which suggested that medium size and long substrates are recognized by residues from both subunits. The identified residues were mutated, and the enzymatic activity of the mutants against sucrose, nystose, and inulin were investigated by kinetic analysis. The replacements that showed the largest effect on catalytic efficiency were Q228V, a residue putatively involved in nystose and inulin binding, and S281I, involved in a polar link at the dimer interface. Moreover, a significant decrease in catalytic efficiency against inulin was observed in the mutants Q435A and Y462A, both located in the beta-sandwich domain of the second monomer. This highlights the essential function that oligomerization plays in substrate specificity and assigns, for the first time, a direct catalytic role to the supplementary domain of a GH32 enzyme.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Invertase
A, B
509Schwanniomyces occidentalisMutation(s): 0 
Gene Names: INV
EC: 3.2.1.26
Find proteins for P24133 (Schwanniomyces occidentalis)
Go to UniProtKB:  P24133
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FRU
Query on FRU

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 60.870α = 90.00
b = 92.270β = 104.81
c = 116.280γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance