5DKY

Crystal structure of glucosidase II alpha subunit (DNJ-bound from)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for two-step glucose trimming by glucosidase II involved in ER glycoprotein quality control.

Satoh, T.Toshimori, T.Yan, G.Yamaguchi, T.Kato, K.

(2016) Sci Rep 6: 20575-20575

  • DOI: 10.1038/srep20575
  • Primary Citation of Related Structures:  5DKX, 5DKZ, 5DL0

  • PubMed Abstract: 
  • The endoplasmic reticulum (ER) has a sophisticated protein quality control system for the efficient folding of newly synthesized proteins. In this system, a variety of N-linked oligosaccharides displayed on proteins serve as signals recognized by ser ...

    The endoplasmic reticulum (ER) has a sophisticated protein quality control system for the efficient folding of newly synthesized proteins. In this system, a variety of N-linked oligosaccharides displayed on proteins serve as signals recognized by series of intracellular lectins. Glucosidase II catalyzes two-step hydrolysis at α1,3-linked glucose-glucose and glucose-mannose residues of high-mannose-type glycans to generate a quality control protein tag that is transiently expressed on glycoproteins and recognized by ER chaperones. Here we determined the crystal structures of the catalytic α subunit of glucosidase II (GIIα) complexed with two different glucosyl ligands containing the scissile bonds of first- and second-step reactions. Our structural data revealed that the nonreducing terminal disaccharide moieties of the two kinds of substrates can be accommodated in a gourd-shaped bilocular pocket, thereby providing a structural basis for substrate-binding specificity in the two-step deglucosylation catalyzed by this enzyme.


    Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha glucosidase-like protein
A
951Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)N/A
Find proteins for G0SG42 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0SG42
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NOJ
Query on NOJ

Download SDF File 
Download CCD File 
A
1-DEOXYNOJIRIMYCIN
MORANOLINE
C6 H13 N O4
LXBIFEVIBLOUGU-JGWLITMVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.155 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 189.523α = 90.00
b = 189.523β = 90.00
c = 157.784γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
JSPS/MEXTJapan24770102, 25121730 to T.S. and 15H02491, 25102008, 24249002 to K.K.
PRESTO/JSTJapan13417569 to T.S.

Revision History 

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2016-02-17
    Type: Database references