EMDB/PDB/SASBDBから引用されている文献のデータベース

キーワード
構造解析手法	All X線回折 NMR 電子顕微鏡小角散乱中性子線回折線維回折粉末回折赤外分光 EPR FRET 理論モデルハイブリッド
著者・登録者
ジャーナル
IF	>30 >20 >10 >5 all

タイトル	Structural basis for transthiolation intermediates in the ubiquitin pathway.
ジャーナル・号・ページ	Nature, Vol. 633, Issue 8028, Page 216-223, Year 2024
掲載日	2024年8月14日
著者	Tomasz Kochańczyk / Zachary S Hann / Michaelyn C Lux / Avelyn Mae V Delos Reyes / Cheng Ji / Derek S Tan / Christopher D Lima /
PubMed 要旨	Transthiolation (also known as transthioesterification) reactions are used in the biosynthesis of acetyl coenzyme A, fatty acids and polyketides, and for post-translational modification by ubiquitin ...Transthiolation (also known as transthioesterification) reactions are used in the biosynthesis of acetyl coenzyme A, fatty acids and polyketides, and for post-translational modification by ubiquitin (Ub) and ubiquitin-like (Ubl) proteins. For the Ub pathway, E1 enzymes catalyse transthiolation from an E1~Ub thioester to an E2~Ub thioester. Transthiolation is also required for transfer of Ub from an E2~Ub thioester to HECT (homologous to E6AP C terminus) and RBR (ring-between-ring) E3 ligases to form E3~Ub thioesters. How isoenergetic transfer of thioester bonds is driven forward by enzymes in the Ub pathway remains unclear. Here we isolate mimics of transient transthiolation intermediates for E1-Ub(T)-E2 and E2-Ub(T)-E3 complexes (where T denotes Ub in a thioester or Ub undergoing transthiolation) using a chemical strategy with native enzymes and near-native Ub to capture and visualize a continuum of structures determined by single-particle cryo-electron microscopy. These structures and accompanying biochemical experiments illuminate conformational changes in Ub, E1, E2 and E3 that are coordinated with the chemical reactions to facilitate directional transfer of Ub from each enzyme to the next.
リンク	Nature / PubMed:39143218 / PubMed Central
手法	EM (単粒子)
解像度	2.5 - 4.16 Å
構造データ	44200 9b55 EMDB-44200, PDB-9b55: Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 1 手法: EM (単粒子) / 解像度: 3.23 Å 44201 9b56 EMDB-44201, PDB-9b56: Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 2 手法: EM (単粒子) / 解像度: 3.35 Å 44202 9b57 EMDB-44202, PDB-9b57: Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 3 手法: EM (単粒子) / 解像度: 3.37 Å 44203 9b58 EMDB-44203, PDB-9b58: Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 4 手法: EM (単粒子) / 解像度: 3.39 Å 44204 9b59 EMDB-44204, PDB-9b59: Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 5 手法: EM (単粒子) / 解像度: 3.49 Å 44205 9b5a EMDB-44205, PDB-9b5a: Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 6 手法: EM (単粒子) / 解像度: 3.65 Å 44206 9b5b EMDB-44206, PDB-9b5b: Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 7 手法: EM (単粒子) / 解像度: 3.31 Å 44207 9b5c EMDB-44207, PDB-9b5c: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - consensus map and model 手法: EM (単粒子) / 解像度: 2.5 Å 44208 9b5d EMDB-44208, PDB-9b5d: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - Ub(T) class 1 map and model from consensus 手法: EM (単粒子) / 解像度: 2.8 Å 44209 9b5e EMDB-44209, PDB-9b5e: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - Ub(T) class 10 map and model from consensus 手法: EM (単粒子) / 解像度: 2.81 Å 44210 9b5f EMDB-44210, PDB-9b5f: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - cluster 1 map and model (Ub(A)/ATP/Mg) 手法: EM (単粒子) / 解像度: 2.78 Å 44211 9b5g EMDB-44211, PDB-9b5g: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - cluster 2 map and model (Ub(A)/ATP/Mg) 手法: EM (単粒子) / 解像度: 2.67 Å 44212 9b5h EMDB-44212, PDB-9b5h: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - cluster 3 map and model (Ub(A)-AMP/PPi/Mg) 手法: EM (単粒子) / 解像度: 2.69 Å 44213 9b5i EMDB-44213, PDB-9b5i: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - cluster 4 map and model (Ub(A)-AMP/PPi/Mg) 手法: EM (単粒子) / 解像度: 2.7 Å 44214 9b5j EMDB-44214, PDB-9b5j: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - cluster 5 map and model (Ub(A)-AMP) 手法: EM (単粒子) / 解像度: 2.86 Å 44215 9b5k EMDB-44215, PDB-9b5k: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - Ub(T) class 1 map and model from cluster 1 (Ub(A)/ATP/Mg) 手法: EM (単粒子) / 解像度: 3.16 Å 44216 9b5l EMDB-44216, PDB-9b5l: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - Ub(T) class 10 map and model from cluster 5 (Ub(A)-AMP) 手法: EM (単粒子) / 解像度: 3.3 Å 44217 9b5m EMDB-44217, PDB-9b5m: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - consensus map and model 手法: EM (単粒子) / 解像度: 2.79 Å 44218 9b5n EMDB-44218, PDB-9b5n: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - Ub(T) class 1 map and model from consensus 手法: EM (単粒子) / 解像度: 3.12 Å 44219 9b5o EMDB-44219, PDB-9b5o: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - Ub(T) class 10 map and model from consensus 手法: EM (単粒子) / 解像度: 3.19 Å 44220 9b5p EMDB-44220, PDB-9b5p: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - cluster 1 map and model (ATP/Mg) 手法: EM (単粒子) / 解像度: 3.08 Å 44221 9b5q EMDB-44221, PDB-9b5q: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - cluster 2 map and model (ATP/Mg) 手法: EM (単粒子) / 解像度: 2.95 Å 44222 9b5r EMDB-44222, PDB-9b5r: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - cluster 3 map and model (ATP/Mg) 手法: EM (単粒子) / 解像度: 2.95 Å 44223 9b5s EMDB-44223, PDB-9b5s: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - cluster 4 map and model (ATP/Mg) 手法: EM (単粒子) / 解像度: 2.96 Å 44224 9b5t EMDB-44224, PDB-9b5t: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - cluster 5 map and model (ATP/Mg) 手法: EM (単粒子) / 解像度: 3.16 Å 44225 9b5u EMDB-44225, PDB-9b5u: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - Ub(T) class 1 map and model from cluster 1 (ATP/Mg) 手法: EM (単粒子) / 解像度: 3.67 Å 44226 9b5v EMDB-44226, PDB-9b5v: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - Ub(T) class 10 map and model from cluster 1 (ATP/Mg) 手法: EM (単粒子) / 解像度: 3.94 Å 44227 9b5w EMDB-44227, PDB-9b5w: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - Ub(T) class 1 map and model from cluster 5 (ATP/Mg) 手法: EM (単粒子) / 解像度: 3.96 Å 44228 9b5x EMDB-44228, PDB-9b5x: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - Ub(T) class 10 map and model from cluster 5 (ATP/Mg) 手法: EM (単粒子) / 解像度: 4.16 Å
化合物	PDB-1aiv: APO OVOTRANSFERRIN ChemComp-MG: Unknown entry / マグネシウムジカチオン ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP / ATP, エネルギー貯蔵分子YM ChemComp-POP: PYROPHOSPHATE 2- ChemComp-AMP: ADENOSINE MONOPHOSPHATE / AMP / AMPYM
由来	schizosaccharomyces pombe 972h- (分裂酵母)
キーワード	LIGASE / UBIQUITIN / E2 / E3 / HECT / NEDD4 / RSP5 / PUB2 / UBC4 / TRANSTHIOESTERIFICATION / THIOESTER / TRANSTHIOLATION / TETRAHEDRAL INTERMEDIATE / ADENYLATION / INHIBITOR / NUCLEUS / PHOSPHOPROTEIN / UBL CONJUGATION PATHWAY / UBL / ATP ATP-BINDING / AMP / NUCLEOTIDE-BINDING / ISOPEPTIDE BOND / E1 / UBA1 / ATP / ATP-binding