8R1M | pdb_00008r1m

Structure of TxGH116 with covalently bound N-azido-octyl aziridine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.227 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.177 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Selective labelling of GBA2 in cells with fluorescent beta-d-arabinofuranosyl cyclitol aziridines.

Su, Q.Louwerse, M.Lammers, R.F.Maurits, E.Janssen, M.Boot, R.G.Borlandelli, V.Offen, W.A.Linzel, D.Schroder, S.P.Davies, G.J.Overkleeft, H.S.Artola, M.Aerts, J.M.F.G.

(2024) Chem Sci 15: 15212-15220

  • DOI: https://doi.org/10.1039/d3sc06146a
  • Primary Citation of Related Structures:  
    8R1M

  • PubMed Abstract: 

    GBA2, the non-lysosomal β-glucosylceramidase, is an enzyme involved in glucosylceramide metabolism. Pharmacological inhibition of GBA2 by N -alkyl iminosugars is well tolerated and benefits patients suffering from Sandhoff and Niemann-Pick type C diseases, and GBA2 inhibitors have been proposed as candidate-clinical drugs for the treatment of parkinsonism. With the ultimate goal to unravel the role of GBA2 in (patho)physiology, we sought to develop a GBA2-specific activity-based probe (ABP). A library of probes was tested for activity against GBA2 and the two other cellular retaining β-glucosidases, lysosomal GBA1 and cytosolic GBA3. We show that β-d-arabinofuranosyl cyclitol aziridine (β-d-Araf aziridine) reacts with the GBA2 active site nucleophile to form a covalent and irreversible bond. Fluorescent β-d-Araf aziridine probes potently and selectively label GBA2 both in vitro and in cellulo , allowing for visualization of the localization of overexpressed GBA2 using fluorescence microscopy. Co-staining with an antibody selective for the lysosomal β-glucosylceramidase GBA1, shows distinct subcellular localization of the two enzymes. We proffer our ABP technology for further delineating the role and functioning of GBA2 in disease and propose the β-d-Araf aziridine scaffold as a good starting point for the development of GBA2-specific inhibitors for clinical development.


  • Organizational Affiliation

    Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden University P. O. Box 9502 2300 RA Leiden The Netherlands j.m.f.g.aerts@lic.leidenuniv.nl m.e.artola@lic.leidenuniv.nl.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glucosylceramidase
A, B
799Thermoanaerobacterium xylanolyticum LX-11Mutation(s): 0 
Gene Names: Thexy_2211
EC: 3.2.1.45
UniProt
Find proteins for F6BL85 (Thermoanaerobacterium xylanolyticum (strain ATCC 49914 / DSM 7097 / LX-11))
Explore F6BL85 
Go to UniProtKB:  F6BL85
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF6BL85
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XHR (Subject of Investigation/LOI)
Query on XHR

Download Ideal Coordinates CCD File 
H [auth A],
K [auth B]
(1R,2R,3R,4S)-4-[8-(azanyldiazenyl)octylamino]-3-(hydroxymethyl)cyclopentane-1,2-diol
C14 H30 N4 O3
FSGISNCKTQXBRQ-IGQOVBAYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
L [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
J [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.227 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.177 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.975α = 90
b = 165.149β = 90
c = 178.921γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union951231

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-02
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Database references, Structure summary