5H18

Crystal structure of catalytic domain of UGGT (UDP-glucose-bound form) from Thermomyces dupontii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Visualisation of a flexible modular structure of the ER folding-sensor enzyme UGGT.

Satoh, T.Song, C.Zhu, T.Toshimori, T.Murata, K.Hayashi, Y.Kamikubo, H.Uchihashi, T.Kato, K.

(2017) Sci Rep 7: 12142-12142

  • DOI: https://doi.org/10.1038/s41598-017-12283-w
  • Primary Citation of Related Structures:  
    5H18, 5Y7F, 5Y7O

  • PubMed Abstract: 

    In the endoplasmic reticulum (ER), a protein quality control system facilitates the efficient folding of newly synthesised proteins. In this system, a series of N-linked glycan intermediates displayed on the protein surface serve as quality tags. The ER folding-sensor enzyme UDP-glucose:glycoprotein glucosyltransferase (UGGT) acts as a gatekeeper in the ER quality control system by specifically catalysing monoglucosylation onto incompletely folded glycoproteins, thereby enabling them to interact with lectin-chaperone complexes. Here we characterise the dynamic structure of this enzyme. Our crystallographic data demonstrate that the sensor region is composed of four thioredoxin-like domains followed by a β-rich domain, which are arranged into a C-shaped structure with a large central cavity, while the C-terminal catalytic domain undergoes a ligand-dependent conformational alteration. Furthermore, small-angle X-ray scattering, cryo-electron microscopy and high-speed atomic force microscopy have demonstrated that UGGT has a flexible modular structure in which the smaller catalytic domain is tethered to the larger folding-sensor region with variable spatial arrangements. These findings provide structural insights into the working mechanism whereby UGGT operates as a folding-sensor against a variety of glycoprotein substrates through its flexible modular structure possessing extended hydrophobic surfaces for the recognition of unfolded substrates.


  • Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan. tadashisatoh@phar.nagoya-cu.ac.jp.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UGGT293Thermomyces dupontiiMutation(s): 0 
UniProt
Find proteins for A0A2D0TCJ6 (Talaromyces thermophilus)
Explore A0A2D0TCJ6 
Go to UniProtKB:  A0A2D0TCJ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2D0TCJ6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.47α = 90
b = 47.24β = 90
c = 129.78γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
SHELXCDphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
MEXTJapan25102001, 25102008
PRESTO, JSTJapan13417569
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Revision History  (Full details and data files)

  • Version 1.0: 2017-09-27
    Type: Initial release
  • Version 1.1: 2017-11-01
    Changes: Database references