7ZLU | pdb_00007zlu

Catalytic domain of UDP-Glucose Glycoprotein Glucosyltransferase from Chaetomium thermophilum in complex with UDP-2-deoxy-2-fluoro-D-glucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.270 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.226 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7ZLU

Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

A quinolin-8-ol sub-millimolar inhibitor of UGGT, the ER glycoprotein folding quality control checkpoint.

Guay, K.P.Ibba, R.Kiappes, J.L.Vasiljevic, S.Boni, F.De Benedictis, M.Zeni, I.Le Cornu, J.D.Hensen, M.Chandran, A.V.Kantsadi, A.L.Caputo, A.T.Blanco Capurro, J.I.Bayo, Y.Hill, J.C.Hudson, K.Lia, A.Brun, J.Withers, S.G.Marti, M.Biasini, E.Santino, A.De Rosa, M.Milani, M.Modenutti, C.P.Hebert, D.N.Zitzmann, N.Roversi, P.

(2023) iScience 26: 107919-107919

  • DOI: https://doi.org/10.1016/j.isci.2023.107919
  • Primary Citation Related Structures: 
    7ZKC, 7ZLL, 7ZLU

  • PubMed Abstract: 

    Misfolded glycoprotein recognition and endoplasmic reticulum (ER) retention are mediated by the ER glycoprotein folding quality control (ERQC) checkpoint enzyme, UDP-glucose glycoprotein glucosyltransferase (UGGT). UGGT modulation is a promising strategy for broad-spectrum antivirals, rescue-of-secretion therapy in rare disease caused by responsive mutations in glycoprotein genes, and many cancers, but to date no selective UGGT inhibitors are known. The small molecule 5-[(morpholin-4-yl)methyl]quinolin-8-ol (5M-8OH-Q) binds a Ct UGGT GT24 "WY" conserved surface motif conserved across UGGTs but not present in other GT24 family glycosyltransferases. 5M-8OH-Q has a 47 μM binding affinity for Ct UGGT GT24 in vitro as measured by ligand-enhanced fluorescence. In cellula , 5M-8OH-Q inhibits both human UGGT isoforms at concentrations higher than 750 μM. 5M-8OH-Q binding to Ct UGGT GT24 appears to be mutually exclusive to M5-9 glycan binding in an in vitro competition experiment. A medicinal program based on 5M-8OH-Q will yield the next generation of UGGT inhibitors.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, and Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, USA.

Macromolecule Content 

  • Total Structure Weight: 108.35 kDa 
  • Atom Count: 7,550 
  • Modeled Residue Count: 834 
  • Deposited Residue Count: 891 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
UDP-glucose-glycoprotein glucosyltransferase-like protein
A, B, C
297Thermochaetoides thermophilaMutation(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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0SB58
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U2F
(Subject of Investigation/LOI)

Query on U2F



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B],
L [auth C]
URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE
C15 H23 F N2 O16 P2
NGTCPFGWXMBZEP-NQQHDEILSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
D [auth A],
I [auth B],
M [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PDO

Query on PDO



Download:Ideal Coordinates CCD File
G [auth A],
K [auth B],
O [auth C]
1,3-PROPANDIOL
C3 H8 O2
YPFDHNVEDLHUCE-UHFFFAOYSA-N
CA
(Subject of Investigation/LOI)

Query on CA



Download:Ideal Coordinates CCD File
F [auth A],
J [auth B],
N [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.270 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.226 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.159α = 110.48
b = 72.316β = 108.33
c = 72.393γ = 108.26
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom106272/Z/14/Z
Wellcome TrustUnited Kingdom204801/Z/16/Z
Wellcome TrustUnited Kingdom214090/Z/18/Z

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-22
    Type: Initial release
  • Version 1.1: 2022-11-30
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references
  • Version 1.3: 2023-10-25
    Changes: Database references
  • Version 1.4: 2024-01-31
    Changes: Refinement description
  • Version 1.5: 2024-11-13
    Changes: Structure summary