8R6B

DTX1 WWE domain in complex with ADP bound to WWE2

Summary for 8R6B

• Entry DOI: 10.2210/pdb8r6b/pdb
• Related: 8R5N
• Descriptor: E3 ubiquitin-protein ligase DTX1, ADENOSINE-5'-DIPHOSPHATE (3 entities in total)
• Functional Keywords: e3 ligase, nucleotide, wwe domain, adp, ligase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 1
• Total formula weight: 19827.22

Authors

Muenzker, L.,Zak, K.M.,Boettcher, J. (deposition date: 2023-11-21, release date: 2024-07-31, Last modification date: 2024-08-07)

Primary citation

Munzker, L.,Kimani, S.W.,Fowkes, M.M.,Dong, A.,Zheng, H.,Li, Y.,Dasovich, M.,Zak, K.M.,Leung, A.K.L.,Elkins, J.M.,Kessler, D.,Arrowsmith, C.H.,Halabelian, L.,Bottcher, J.
A ligand discovery toolbox for the WWE domain family of human E3 ligases.
Commun Biol, 7:901-901, 2024

PubMed Abstract: The WWE domain is a relatively under-researched domain found in twelve human proteins and characterized by a conserved tryptophan-tryptophan-glutamate (WWE) sequence motif. Six of these WWE domain-containing proteins also contain domains with E3 ubiquitin ligase activity. The general recognition of poly-ADP-ribosylated substrates by WWE domains suggests a potential avenue for development of Proteolysis-Targeting Chimeras (PROTACs). Here, we present novel crystal structures of the HUWE1, TRIP12, and DTX1 WWE domains in complex with PAR building blocks and their analogs, thus enabling a comprehensive analysis of the PAR binding site structural diversity. Furthermore, we introduce a versatile toolbox of biophysical and biochemical assays for the discovery and characterization of novel WWE domain binders, including fluorescence polarization-based PAR binding and displacement assays, N-NMR-based binding affinity assays and F-NMR-based competition assays. Through these assays, we have characterized the binding of monomeric iso-ADP-ribose (iso-ADPr) and its nucleotide analogs with the aforementioned WWE proteins. Finally, we have utilized the assay toolbox to screen a small molecule fragment library leading to the successful discovery of novel ligands targeting the HUWE1 WWE domain.

PubMed: 39048679
DOI: 10.1038/s42003-024-06584-w

Experimental method

X-RAY DIFFRACTION (2.5 Å)