3WWG

Crystal structure of the N-glycan-deficient variant N448A of isopullulanase complexed with isopanose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The side chain of a glycosylated asparagine residue is important for the stability of isopullulanase

Miyazaki, T.Yashiro, H.Nishikawa, A.Tonozuka, T.

(2015) J.Biochem. 157: 225-234

  • DOI: 10.1093/jb/mvu065

  • PubMed Abstract: 
  • N-glycosylation has been shown to be important for the stability of some glycoproteins. Isopullulanase (IPU), a polysaccharide-hydrolyzing enzyme, is a highly N-glycosylated protein, and IPU deglycosylation results in a decrease in thermostability. T ...

    N-glycosylation has been shown to be important for the stability of some glycoproteins. Isopullulanase (IPU), a polysaccharide-hydrolyzing enzyme, is a highly N-glycosylated protein, and IPU deglycosylation results in a decrease in thermostability. To investigate the function of N-glycan in IPU, we focused on an N-glycosylated residue located in the vicinity of the active site, Asn448. The thermostabilities of three IPU variants, Y440A, N448A and S450A, were 0.5-8.4°C lower than the wild-type enzyme. The crystal structure of endoglycosidase H (Endo H)-treated N448A variant was determined. There are four IPU molecules, Mol-A, B, C and D, in the asymmetric unit. The conformation of a loop composed of amino acid residues 435-455 in Mol-C was identical to wild-type IPU, whereas the conformations of this loop in Mol-A, Mol-B and Mol-D were different from each other. These results suggest that the Asn448 side chain is primarily important for the stability of IPU. Our results indicate that mutation of only N-glycosylated Asn residue may lead to incorrect conclusion for the evaluation of the function of N-glycan. Usually, the structures of N-glycosylation sites form an extended configuration in IPU; however, the Asn448 site had an atypical structure that lacked this configuration.


    Organizational Affiliation

    Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan tonozuka@cc.tuat.ac.jp.,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, C, D
549Aspergillus nigerMutation(s): 1 
Gene Names: ipuA
EC: 3.2.1.57
Find proteins for O00105 (Aspergillus niger)
Go to UniProtKB:  O00105
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAL
Query on MAL

Download SDF File 
Download CCD File 
C
MALTOSE
C12 H22 O11
GUBGYTABKSRVRQ-ASMJPISFSA-N
 Ligand Interaction
BGC
Query on BGC

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Download CCD File 
B
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
GLC
Query on GLC

Download SDF File 
Download CCD File 
B
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 96.400α = 90.00
b = 108.100β = 103.90
c = 116.000γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
MOLREPphasing
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-12
    Type: Initial release
  • Version 1.1: 2015-04-15
    Type: Database references