9O4M

Crystal structure of Ubiquitin Carboxy Terminal Hydrolase L1 Q209C mutant covalently crosslinked to ubiquitin genetically encoded with N6-(6-bromohexanoyl)-L-lysine

9O4M の概要

• エントリーDOI: 10.2210/pdb9o4m/pdb
• 分子名称: Polyubiquitin-C, Ubiquitin carboxyl-terminal hydrolase isozyme L1, HEXANOIC ACID, ... (4 entities in total)
• 機能のキーワード: uchl1, genetic code expansion, covalent trapping, unnatural amino acid, ubiquitin, hydrolase
• 由来する生物種: Homo sapiens (human); 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 67102.84

構造登録者

Pannala, N.,Patel, R.,Das, C. (登録日: 2025-04-08, 公開日: 2025-07-30, 最終更新日: 2025-12-03)

主引用文献

Pannala, N.M.,Patel, R.S.,Anit, A.S.,Bhattacharya, D.,Teron, K.N.,Drown, B.,Fasan, R.,Das, C.
Internal Ubiquitin Electrophiles for Covalent Trapping and Inhibition of Deubiquitinases.
Chembiochem, 26:e202500318-e202500318, 2025

PubMed Abstract: The ubiquitin (Ub) system governs vital cellular processes in eukaryotic biology through an intricate network of Ub-protein interactions. While semisynthetic C-terminal Ub electrophiles (UbEs) are widely used to study Ub transfer and deubiquitinase (Dub) activity, they are limited to probing the active site while leaving other functionally important sites unexplored. Building on previously identified multivalent interaction interfaces and potential allosteric sites which are key to understanding their dynamic nature, here we report the development of genetically encoded Ub-based probes to covalently tether Ub-protein interactions in a proximity-driven manner at distal locations away from the active site. This study demonstrates that UbEs with internal electrophiles maintain conformational changes observed with their C-terminal counterparts while circumventing their limitations in capturing distal binding-site complexes, an emerging feature in Ub-mediated regulation. Genetically encoding these electrophiles further demonstrate rational variation as activity-based probes (ABP), leading to a Met1-diUb ABP showing preference for OTULIN over other Met1 cleaving Dubs. Taken together, our study introduces genetically encoded Ub-based probes to explore the structural and biochemical significance of Ub-Dub interactions beyond the canonical S1 site, overcoming some limitations of traditional Ub C-terminal electrophiles.

PubMed: 40626928
DOI: 10.1002/cbic.202500318

実験手法

X-RAY DIFFRACTION (2 Å)