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	A unified view on enzyme catalysis by cryo-EM study of a DNA topoisomerase.
ジャーナル・号・ページ	Commun Chem, Vol. 7, Issue 1, Page 45, Year 2024
掲載日	2024年2月28日
著者	Chiung-Wen Mary Chang / Shun-Chang Wang / Chun-Hsiung Wang / Allan H Pang / Cheng-Han Yang / Yao-Kai Chang / Wen-Jin Wu / Ming-Daw Tsai /
PubMed 要旨	The theories for substrate recognition in enzyme catalysis have evolved from lock-key to induced fit, then conformational selection, and conformational selection followed by induced fit. However, the ...The theories for substrate recognition in enzyme catalysis have evolved from lock-key to induced fit, then conformational selection, and conformational selection followed by induced fit. However, the prevalence and consensus of these theories require further examination. Here we use cryogenic electron microscopy and African swine fever virus type 2 topoisomerase (AsfvTop2) to demonstrate substrate binding theories in a joint and ordered manner: catalytic selection by the enzyme, conformational selection by the substrates, then induced fit. The apo-AsfvTop2 pre-exists in six conformers that comply with the two-gate mechanism directing DNA passage and release in the Top2 catalytic cycle. The structures of AsfvTop2-DNA-inhibitor complexes show that substantial induced-fit changes occur locally from the closed apo-conformer that however is too far-fetched for the open apo-conformer. Furthermore, the ATPase domain of AsfvTop2 in the MgAMP-PNP-bound crystal structures coexist in reduced and oxidized forms involving a disulfide bond, which can regulate the AsfvTop2 function.
リンク	Commun Chem / PubMed:38418525 / PubMed Central
手法	EM (単粒子) / X線回折
解像度	1.14 - 3.68 Å
構造データ	36062 8j87 EMDB-36062, PDB-8j87: Asfv topoisomerase 2 - apo conformer Ia 手法: EM (単粒子) / 解像度: 3.42 Å 36063 8j88 EMDB-36063, PDB-8j88: Asfv topoisomerase 2 - apo conformer Ib 手法: EM (単粒子) / 解像度: 3.49 Å 36064 8j89 EMDB-36064, PDB-8j89: Cryo-EM structure of Asfv topoisomerase 2 - apo conformer IIa 手法: EM (単粒子) / 解像度: 2.31 Å 36065 8j8a EMDB-36065, PDB-8j8a: Cryo-EM structure of Asfv topoisomerase 2 - apo conformer IIb 手法: EM (単粒子) / 解像度: 2.51 Å 36066 8j8b EMDB-36066, PDB-8j8b: Cryo-EM structure of Asfv topoisomerase 2 - apo conformer IIIa 手法: EM (単粒子) / 解像度: 2.43 Å 36067 8j8c EMDB-36067, PDB-8j8c: Cryo-EM structure of Asfv topoisomerase 2 - apo conformer IIIb 手法: EM (単粒子) / 解像度: 2.69 Å 36116 8j9v EMDB-36116, PDB-8j9v: Cryo-EM structure of the African swine fever virus topoisomerase 2 complexed with Cut02aDNA and etoposide (EDI-1) 手法: EM (単粒子) / 解像度: 2.71 Å 36117 8j9w EMDB-36117, PDB-8j9w: Cryo-EM structure of the African swine fever virus topoisomerase 2 complexed with Cut02bDNA and etoposide (EDI-2) 手法: EM (単粒子) / 解像度: 2.76 Å 36118 8j9x EMDB-36118, PDB-8j9x: Cryo-EM structure of the African swine fever virus topoisomerase 2 complexed with Cut02aDNA and m-AMSA (EDI-3) 手法: EM (単粒子) / 解像度: 3.0 Å EMDB-36473: Cryo-EM structure of the full-length African swine fever virus topoisomerase 2 complexed with Cut02aDNA and etoposide 手法: EM (単粒子) / 解像度: 3.68 Å PDB-8ja1: ASFV Topoisomerase ATPase domain in complex with AMP-PNP and Mg2+ (oxidized form) 手法: X-RAY DIFFRACTION / 解像度: 1.14 Å PDB-8ja2: ASFV Topoisomerase ATPase domain in complex with AMP-PNP and Mg2+ 手法: X-RAY DIFFRACTION / 解像度: 1.73 Å
化合物	ChemComp-MG: Unknown entry / マグネシウムジカチオン ChemComp-EVP: (5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol / エトポシド / 薬剤, 化学療法薬YM / エトポシド ChemComp-ASW: N-[4-(acridin-9-ylamino)-3-methoxyphenyl]methanesulfonamide / アムサクリン / 抗腫瘍剤YM / Amsacrine ChemComp-ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP / AMP-PNP, エネルギー貯蔵分子類似体YM ChemComp-HOH*: WATER / 水
由来	african swine fever virus (アフリカ豚コレラウイルス) homo sapiens (ヒト)
キーワード	ISOMERASE (異性化酵素) / Topoisomerase (DNAトポイソメラーゼ) / ASFV (アフリカ豚熱ウイルス) / VIRAL PROTEIN (ウイルスタンパク質) / ISOMERASE/DNA / inhibitor (酵素阻害剤) / ISOMERASE-DNA complex / GHKL NUCLEOTIDE-BINDING FOLD / AMP-PNP