1Y4W

Crystal structure of exo-inulinase from Aspergillus awamori in spacegroup P21


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of exo-inulinase from Aspergillus awamori: the enzyme fold and structural determinants of substrate recognition

Nagem, R.A.P.Rojas, A.L.Golubev, A.M.Korneeva, O.S.Eneyskaya, E.V.Kulminskaya, A.A.Neustroev, K.N.Polikarpov, I.

(2004) J.Mol.Biol. 344: 471-480

  • DOI: 10.1016/j.jmb.2004.09.024
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Exo-inulinases hydrolyze terminal, non-reducing 2,1-linked and 2,6-linked beta-d-fructofuranose residues in inulin, levan and sucrose releasing beta-d-fructose. We present the X-ray structure at 1.55A resolution of exo-inulinase from Aspergillus awam ...

    Exo-inulinases hydrolyze terminal, non-reducing 2,1-linked and 2,6-linked beta-d-fructofuranose residues in inulin, levan and sucrose releasing beta-d-fructose. We present the X-ray structure at 1.55A resolution of exo-inulinase from Aspergillus awamori, a member of glycoside hydrolase family 32, solved by single isomorphous replacement with the anomalous scattering method using the heavy-atom sites derived from a quick cryo-soaking technique. The tertiary structure of this enzyme folds into two domains: the N-terminal catalytic domain of an unusual five-bladed beta-propeller fold and the C-terminal domain folded into a beta-sandwich-like structure. Its structural architecture is very similar to that of another member of glycoside hydrolase family 32, invertase (beta-fructosidase) from Thermotoga maritima, determined recently by X-ray crystallography The exo-inulinase is a glycoprotein containing five N-linked oligosaccharides. Two crystal forms obtained under similar crystallization conditions differ by the degree of protein glycosylation. The X-ray structure of the enzyme:fructose complex, at a resolution of 1.87A, reveals two catalytically important residues: Asp41 and Glu241, a nucleophile and a catalytic acid/base, respectively. The distance between the side-chains of these residues is consistent with a double displacement mechanism of reaction. Asp189, which is part of the Arg-Asp-Pro motif, provides hydrogen bonds important for substrate recognition.


    Related Citations: 
    • Purification, characterization, gene cloning and preliminary X-ray data of the exo-inulinase from Aspergillus awamori
      Arand, M.,Golubev, A.M.,Neto, J.R.,Polikarpov, I.,Wattiez, R.,Korneeva, O.S.,Eneyskaya, E.V.,Kulminskaya, A.A.,Shabalin, K.A.,Shishliannikov, S.M.,Chepurnaya, O.V.,Neustroev, K.N.
      (2002) BIOCHEM.J. 362: 131


    Organizational Affiliation

    Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-carlense 400, CEP 13560-970, São Carlos, SP, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
exo-inulinase
A
518Aspergillus awamoriMutation(s): 0 
Gene Names: inuE (inu1)
EC: 3.2.1.80
Find proteins for Q96TU3 (Aspergillus awamori)
Go to UniProtKB:  Q96TU3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 49.954α = 90.00
b = 94.029β = 107.04
c = 67.634γ = 90.00
Software Package:
Software NamePurpose
SHARPphasing
REFMACrefinement
SCALEPACKdata scaling
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description