1X0C

Improved Crystal Structure of Isopullulanase from Aspergillus niger ATCC 9642


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of Aspergillus niger Isopullulanase, a Member of Glycoside Hydrolase Family 49

Mizuno, M.Koide, A.Yamamura, A.Akeboshi, H.Yoshida, H.Kamitori, S.Sakano, Y.Nishikawa, A.Tonozuka, T.

(2008) J.Mol.Biol. 376: 210-220

  • DOI: 10.1016/j.jmb.2007.11.098
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • An isopullulanase (IPU) from Aspergillus niger ATCC9642 hydrolyzes alpha-1,4-glucosidic linkages of pullulan to produce isopanose. Although IPU does not hydrolyze dextran, it is classified into glycoside hydrolase family 49 (GH49), major members of w ...

    An isopullulanase (IPU) from Aspergillus niger ATCC9642 hydrolyzes alpha-1,4-glucosidic linkages of pullulan to produce isopanose. Although IPU does not hydrolyze dextran, it is classified into glycoside hydrolase family 49 (GH49), major members of which are dextran-hydrolyzing enzymes. IPU is highly glycosylated, making it difficult to obtain its crystal. We used endoglycosidase H(f) to cleave the N-linked oligosaccharides of IPU, and we here determined the unliganded and isopanose-complexed forms of IPU, both solved at 1.7-A resolution. IPU is composed of domains N and C joined by a short linker, with electron density maps for 11 or 12 N-acetylglucosamine residues per molecule. Domain N consists of 13 beta-strands and forms a beta-sandwich. Domain C, where the active site is located, forms a right-handed beta-helix, and the lengths of the pitches of each coil of the beta-helix are similar to those of GH49 dextranase and GH28 polygalacturonase. The entire structure of IPU resembles that of a GH49 enzyme, Penicillium minioluteum dextranase (Dex49A), despite a difference in substrate specificity. Compared with the active sites of IPU and Dex49A, the amino acid residues participating in subsites +2 and +3 are not conserved, and the glucose residues of isopanose bound to IPU completely differ in orientation from the corresponding glucose residues of isomaltose bound to Dex49A. The shape of the catalytic cleft characterized by the seventh coil of the beta-helix and a loop from domain N appears to be critical in determining the specificity of IPU for pullulan.


    Organizational Affiliation

    Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-Cho, Fuchu, Tokyo 183-8509, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Isopullulanase
A, B
549Aspergillus nigerMutation(s): 0 
Gene Names: ipuA
EC: 3.2.1.57
Find proteins for O00105 (Aspergillus niger)
Go to UniProtKB:  O00105
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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: 1.7 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 99.725α = 90.00
b = 136.158β = 90.00
c = 84.473γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
MOLREPphasing
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-06-13
    Type: Initial release
  • Version 1.1: 2008-01-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance