9GN8 の概要
| エントリーDOI | 10.2210/pdb9gn8/pdb |
| 関連するPDBエントリー | 2Z6O 7NVJ |
| 分子名称 | Ubiquitin-fold modifier-conjugating enzyme 1, 1,2-ETHANEDIOL, FORMIC ACID, ... (5 entities in total) |
| 機能のキーワード | ufm1 conjugating enzyme activity, ubc core domain containing protein, brain development, infantile encephalopathy, ligase |
| 由来する生物種 | Homo sapiens (human) |
| タンパク質・核酸の鎖数 | 1 |
| 化学式量合計 | 19849.65 |
| 構造登録者 | |
| 主引用文献 | Kumar, M.,Banerjee, S.,Cohen-Kfir, E.,Mitelberg, M.B.,Tiwari, S.,Isupov, M.N.,Dessau, M.,Wiener, R. UFC1 reveals the multifactorial and plastic nature of oxyanion holes in E2 conjugating enzymes. Nat Commun, 16:3912-3912, 2025 Cited by PubMed Abstract: The conjugation of ubiquitin (Ub) or ubiquitin-like proteins (UBL) to target proteins is a crucial post-translational modification that typically involves nucleophilic attack by a lysine on a charged E2 enzyme (E2~Ub/UBL), forming an oxyanion intermediate. Stabilizing this intermediate through an oxyanion hole is vital for progression of the reaction. Still, the mechanism of oxyanion stabilization in E2 enzymes remains unclear, although an asparagine residue in the conserved HPN motif of E2 enzymes was suggested to stabilize the oxyanion intermediate. Here, we study the E2 enzyme UFC1, which presents a TAK rather than an HPN motif. Crystal structures of UFC1 mutants, including one that mimics the oxyanion intermediate, combined with in vitro activity assays, suggest that UFC1 utilizes two distinct types of oxyanion holes, one that stabilizes the oxyanion intermediate during trans-ufmylation mediated by the E3 ligase, and another that stabilizes cis-driven auto-ufmylation. Our findings indicate that oxyanion stabilization is influenced by multiple factors, including C-alpha hydrogen bonding, and is adaptable, enabling different modes of action. PubMed: 40280917DOI: 10.1038/s41467-025-58826-y 主引用文献が同じPDBエントリー |
| 実験手法 | X-RAY DIFFRACTION (1.96 Å) |
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