8J0A

Robust design of effective allosteric activator UbV R4 for Rsp5 E3 ligase using the machine-learning tool ProteinMPNN

8J0A の概要

• エントリーDOI: 10.2210/pdb8j0a/pdb
• 分子名称: Ubiquitin variant R4, SULFATE ION (3 entities in total)
• 機能のキーワード: ubiquitin variant, deep-learning, biosynthetic protein
• 由来する生物種: synthetic construct
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 23620.53

構造登録者

Lin, Y.-F.,Hsieh, Y.-J.,Kao, H.-W.,Ko, T.-P.,Wu, K.-P. (登録日: 2023-04-10, 公開日: 2023-08-09, 最終更新日: 2023-08-30)

主引用文献

Kao, H.W.,Lu, W.L.,Ho, M.R.,Lin, Y.F.,Hsieh, Y.J.,Ko, T.P.,Danny Hsu, S.T.,Wu, K.P.
Robust Design of Effective Allosteric Activators for Rsp5 E3 Ligase Using the Machine Learning Tool ProteinMPNN.
Acs Synth Biol, 12:2310-2319, 2023

PubMed Abstract: We used the deep learning tool ProteinMPNN to redesign ubiquitin (Ub) as a specific and functionally stimulating/enhancing binder of the Rsp5 E3 ligase. We generated 20 extensively mutated─up to 37 of 76 residues─recombinant Ub variants (UbVs), named R1 to R20, displaying well-folded structures and high thermal stabilities. These UbVs can also form stable complexes with Rsp5, as predicted using AlphaFold2. Three of the UbVs bound to Rsp5 with low micromolar affinity, with R4 and R12 effectively enhancing the Rsp5 activity six folds. AlphaFold2 predicts that R4 and R12 bind to Rsp5's exosite in an identical manner to the Rsp5-Ub template, thereby allosterically activating Rsp5-Ub thioester formation. Thus, we present a virtual solution for rapidly and cost-effectively designing UbVs as functional modulators of Ub-related enzymes.

PubMed: 37556858
DOI: 10.1021/acssynbio.3c00042

実験手法

X-RAY DIFFRACTION (3 Å)