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8VK8

Structure of UbV.d2.1 in complex with Ube2d2

Summary for 8VK8
Entry DOI10.2210/pdb8vk8/pdb
DescriptorUbiquitin-conjugating enzyme E2 D2, Ubiquitin variant D2.1 (2 entities in total)
Functional Keywordsubiquitin conjugating enzyme, ubiquitin variant, e2 enzyme, inhibitor, transferase
Biological sourceHomo sapiens (human)
More
Total number of polymer chains8
Total formula weight103228.50
Authors
Middleton, A.J. (deposition date: 2024-01-08, release date: 2024-09-25, Last modification date: 2024-11-13)
Primary citationMcAlpine, J.M.R.B.,Zhu, G.,Pudjihartono, N.,Teyra, J.,Currie, M.J.,Tillett, Z.D.,Dobson, R.C.J.,Sidhu, S.S.,Day, C.L.,Middleton, A.J.
Structural and biophysical characterisation of ubiquitin variants that inhibit the ubiquitin conjugating enzyme Ube2d2.
Febs J., 2024
Cited by
PubMed Abstract: The ubiquitin-conjugating E2 enzymes play a central role in ubiquitin transfer. Disruptions to the ubiquitin system are implicated in multiple diseases, and as a result, molecules that modulate the activity of the ubiquitin system are of interest. E2 enzyme function relies on interactions with partner proteins, and the disruption of these is an effective way to modulate activity. Here, we report the discovery of ubiquitin variants (UbVs) that inhibit the E2 enzyme, Ube2d2 (UbcH5b). The six UbVs identified inhibit ubiquitin chain building, and the structural and biophysical characterisation of two of these demonstrate they bind to Ube2d2 with low micromolar affinity and high specificity. Both characterised UbVs bind at a site that overlaps with E1 binding, while the more inhibitory UbV has an additional binding site that blocks a critical non-covalent ubiquitin-binding site on the E2 enzyme. The discovery of novel protein-based ubiquitin derivatives that inhibit protein-protein interactions is an important step towards discovering small molecules that inhibit the activity of E2 enzymes. Furthermore, the specificity of the UbVs within the Ube2d family suggests that it may be possible to develop tools to selectively inhibit highly related E2 enzymes.
PubMed: 39473070
DOI: 10.1111/febs.17311
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (2.99 Å)
Structure validation

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건을2024-11-13부터공개중

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