5OXD

Complex of a C. perfringens O-GlcNAcase with a fragment hit

Summary for 5OXD

• Entry DOI: 10.2210/pdb5oxd/pdb
• Descriptor: O-GlcNAcase NagJ, CADMIUM ION, 5-(trifluoromethyl)-2,3-dihydro-1~{H}-1,4-diazepine, ... (4 entities in total)
• Functional Keywords: hydrolase, fragment complex, carbohydrate
• Biological source: Clostridium perfringens
• Total number of polymer chains: 1
• Total formula weight: 68768.16

Authors

Rafie, K.,van Aalten, D.M.F. (deposition date: 2017-09-06, release date: 2018-05-16, Last modification date: 2024-01-17)

Primary citation

Borodkin, V.S.,Rafie, K.,Selvan, N.,Aristotelous, T.,Navratilova, I.,Ferenbach, A.T.,van Aalten, D.M.F.
O-GlcNAcase Fragment Discovery with Fluorescence Polarimetry.
ACS Chem. Biol., 13:1353-1360, 2018

PubMed Abstract: The attachment of the sugar N-acetyl-D-glucosamine (GlcNAc) to specific serine and threonine residues on proteins is referred to as protein O-GlcNAcylation. O-GlcNAc transferase (OGT) is the enzyme responsible for carrying out the modification, while O-GlcNAcase (OGA) reverses it. Protein O-GlcNAcylation has been implicated in a wide range of cellular processes including transcription, proteostasis, and stress response. Dysregulation of O-GlcNAc has been linked to diabetes, cancer, and neurodegenerative and cardiovascular disease. OGA has been proposed to be a drug target for the treatment of Alzheimer's and cardiovascular disease given that increased O-GlcNAc levels appear to exert a protective effect. The search for specific, potent, and drug-like OGA inhibitors with bioavailability in the brain is therefore a field of active research, requiring orthogonal high-throughput assay platforms. Here, we describe the synthesis of a novel probe for use in a fluorescence polarization based assay for the discovery of inhibitors of OGA. We show that the probe is suitable for use with both human OGA, as well as the orthologous bacterial counterpart from Clostridium perfringens, CpOGA, and the lysosomal hexosaminidases HexA/B. We structurally characterize CpOGA in complex with a ligand identified from a fragment library screen using this assay. The versatile synthesis procedure could be adapted for making fluorescent probes for the assay of other glycoside hydrolases.

PubMed: 29641181
DOI: 10.1021/acschembio.8b00183

Experimental method

X-RAY DIFFRACTION (2.6 Å)