5DKY | pdb_00005dky

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

• PDB DOI: https://doi.org/10.2210/pdb5DKY/pdb

• Classification: HYDROLASE
• Organism(s): Thermochaetoides thermophila DSM 1495
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-09-04 Released: 2016-01-27 
• Deposition Author(s): Satoh, T., Toshimori, T., Yan, G., Yamaguchi, T., Kato, K.
• Funding Organization(s): JSPS/MEXT, PRESTO/JST

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.184 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

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

• PubMed: 26847925 
• DOI: https://doi.org/10.1038/srep20575
• Primary Citation Related Structures: 
  5DKX, 5DKY, 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 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.

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Organizational Affiliation: 
• Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan.
JST, PRESTO, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan.
Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan.
School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 108.66 kDa 
• Atom Count: 8,336 
• Modeled Residue Count: 928 
• Deposited Residue Count: 951 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha glucosidase-like protein	A	951	Thermochaetoides thermophila DSM 1495	Mutation(s): 0  Gene Names: CTHT_0064960 EC: 3.2.1.20
UniProt
Find proteins for G0SG42 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0SG42  Go to UniProtKB:  G0SG42

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NOJ	B [auth A]	1-DEOXYNOJIRIMYCIN C6 H13 N O4 LXBIFEVIBLOUGU-JGWLITMVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.184 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 189.523	α = 90
b = 189.523	β = 90
c = 157.784	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-01-27 
Deposition Author(s): Satoh, T., Toshimori, T., Yan, G., Yamaguchi, T., Kato, K.

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Funding Organization	Location	Grant Number
JSPS/MEXT	Japan	24770102, 25121730 to T.S. and 15H02491, 25102008, 24249002 to K.K.
PRESTO/JST	Japan	13417569 to T.S.

Revision History  

• Version 1.0: 2016-01-27
  Type: Initial release
  
• Version 1.1: 2016-02-17
  Changes: Database references
• Version 1.2: 2020-02-19
  Changes: Data collection, Derived calculations
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references