5Y7F | pdb_00005y7f

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

• PDB DOI: https://doi.org/10.2210/pdb5Y7F/pdb

• Classification: TRANSFERASE
• Organism(s): Thermomyces dupontii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-08-17 Released: 2017-09-27 
• Deposition Author(s): Satoh, T., Song, C., Zhu, T., Toshimori, T., Murata, K., Hayashi, Y., Kamikubo, H., Uchihashi, T., Kato, K.
• Funding Organization(s): MEXT, KAKENHI, JST, PRESTO

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.208 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

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

• PubMed: 28939828 
• DOI: https://doi.org/10.1038/s41598-017-12283-w
• Primary Citation 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. [e-mail].
JST, PRESTO, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan. [e-mail].
National Institute for Physiological Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan.
Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan.
Okazaki Institute for Integrative Bioscience, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan.
Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan.
School of Physical Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan.
School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan.
Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan.
Department of Physics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.
Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan. [e-mail].
Okazaki Institute for Integrative Bioscience, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan. [e-mail].
Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan. [e-mail].
School of Physical Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 35.66 kDa 
• Atom Count: 2,494 
• Modeled Residue Count: 267 
• Deposited Residue Count: 293 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UGGT	A	293	Thermomyces dupontii	Mutation(s): 0
UniProt
Find proteins for A0A2D0TCJ6 (Talaromyces thermophilus) Explore A0A2D0TCJ6  Go to UniProtKB:  A0A2D0TCJ6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP	B [auth A]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
TRS	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.208 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.41	α = 90
b = 46.85	β = 90
c = 131.99	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-09-27 
Deposition Author(s): Satoh, T., Song, C., Zhu, T., Toshimori, T., Murata, K., Hayashi, Y., Kamikubo, H., Uchihashi, T., Kato, K.

---

Funding Organization	Location	Grant Number
MEXT, KAKENHI	Japan	JP25102008
MEXT, KAKENHI	Japan	JP25102001
JST, PRESTO	Japan	JPMJPR13L5

Revision History  

• Version 1.0: 2017-09-27
  Type: Initial release
  
• Version 1.1: 2017-11-01
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary