8R1M | pdb_00008r1m

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

PDB DOI: https://doi.org/10.2210/pdb8R1M/pdb

Classification: HYDROLASE
Organism(s): Thermoanaerobacterium xylanolyticum LX-11
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-11-02 Released: 2024-10-02
Deposition Author(s): Offen, W.A., Davies, G.J.
Funding Organization(s): European Research Council (ERC)

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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wwPDB Validation 3D Report Full Report

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

PubMed: 39246358 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1039/d3sc06146a
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 184.67 kDa
Atom Count: 13,525
Modeled Residue Count: 1,544
Deposited Residue Count: 1,598
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosylceramidase	A, B	799	Thermoanaerobacterium xylanolyticum LX-11	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F6BL85
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XHR (Subject of Investigation/LOI) Query on XHR Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A]	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		Interactions Focus chain H [auth A] Focus chain K [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B]	F [auth A], G [auth A], L [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain C [auth A]	C [auth A], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B]