Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 344.15 kDa 
• Atom Count: 22447 
• Modelled Residue Count: 2754 
• Deposited Residue Count: 2988 
• Unique protein chains: 1

5N2J

UDP-Glucose Glycoprotein Glucosyltransferase from Chaetomium thermophilum (closed form)

• PDB DOI: 10.2210/pdb5N2J/pdb

• Classification: TRANSFERASE
• Organism(s): Chaetomium thermophilum var. thermophilum DSM 1495
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2017-02-07 Released: 2017-07-26 
• Deposition Author(s): Roversi, P., Caputo, A.T., Hill, J., Alonzi, D.S., Zitzmann, N.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.40 Å
• R-Value Free: 0.259 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 

Literature

Interdomain conformational flexibility underpins the activity of UGGT, the eukaryotic glycoprotein secretion checkpoint.

Roversi, P., Marti, L., Caputo, A.T., Alonzi, D.S., Hill, J.C., Dent, K.C., Kumar, A., Levasseur, M.D., Lia, A., Waksman, T., Basu, S., Soto Albrecht, Y., Qian, K., McIvor, J.P., Lipp, C.B., Siliqi, D., Vasiljevic, S., Mohammed, S., Lukacik, P., Walsh, M.A., Santino, A., Zitzmann, N.

(2017) Proc Natl Acad Sci U S A 114: 8544-8549

• PubMed: 28739903 
• DOI: 10.1073/pnas.1703682114
• Primary Citation of Related Structures:  
  5MU1, 5MZO, 5N2J, 5NV4


• PubMed Abstract: 
  

Glycoproteins traversing the eukaryotic secretory pathway begin life in the endoplasmic reticulum (ER), where their folding is surveyed by the 170-kDa UDP-glucose:glycoprotein glucosyltransferase (UGGT). The enzyme acts as the single glycoprotein folding quality control checkpoint: it selectively reglucosylates misfolded glycoproteins, promotes their association with ER lectins and associated chaperones, and prevents premature secretion from the ER. UGGT has long resisted structural determination and sequence-based domain boundary prediction. Questions remain on how this single enzyme can flag misfolded glycoproteins of different sizes and shapes for ER retention and how it can span variable distances between the site of misfold and a glucose-accepting N-linked glycan on the same glycoprotein. Here, crystal structures of a full-length eukaryotic UGGT reveal four thioredoxin-like (TRXL) domains arranged in a long arc that terminates in two β-sandwiches tightly clasping the glucosyltransferase domain. The fold of the molecule is topologically complex, with the first β-sandwich and the fourth TRXL domain being encoded by nonconsecutive stretches of sequence. In addition to the crystal structures, a 15-Å cryo-EM reconstruction reveals interdomain flexibility of the TRXL domains. Double cysteine point mutants that engineer extra interdomain disulfide bridges rigidify the UGGT structure and exhibit impaired activity. The intrinsic flexibility of the TRXL domains of UGGT may therefore endow the enzyme with the promiscuity needed to recognize and reglucosylate its many different substrates and/or enable reglucosylation of N-linked glycans situated at variable distances from the site of misfold.

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Organizational Affiliation: 

Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom; [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glucose-glycoprotein glucosyltransferase-like protein	A, B	1494	Chaetomium thermophilum var. thermophilum DSM 1495	Mutation(s): 0  Gene Names: CTHT_0048990
UniProt
Find proteins for G0SB58 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0SB58  Go to UniProtKB:  G0SB58

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, F	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, G	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G77367MI GlyCosmos:  G77367MI GlyGen:  G77367MI

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, H	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	I [auth A], J [auth A], M [auth B], N [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO	L [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	K [auth A], O [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.40 Å
• R-Value Free: 0.259 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.6	α = 90
b = 148.6	β = 90
c = 179.97	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-02-07 
• Released Date: 2017-07-26 
Deposition Author(s): Roversi, P., Caputo, A.T., Hill, J., Alonzi, D.S., Zitzmann, N.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	097300/Z/11/Z
Wellcome Trust	United Kingdom	106272/Z/14/Z

Revision History  

• Version 1.0: 2017-07-26
  Type: Initial release
  
• Version 1.1: 2017-08-02
  Changes: Database references
• Version 1.2: 2017-08-16
  Changes: Database references
• Version 1.3: 2017-11-29
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary