8J9W

Cryo-EM structure of the African swine fever virus topoisomerase 2 complexed with Cut02bDNA and etoposide (EDI-2)

8J9W の概要

• エントリーDOI: 10.2210/pdb8j9w/pdb
• EMDBエントリー: 36117
• 分子名称: DNA topoisomerase 2, DNA (5'-D(*AP*AP*GP*AP*AP*CP*TP*CP*TP*GP*TP*AP*G)-3'), DNA (5'-D(*CP*AP*TP*GP*CP*TP*AP*CP*AP*GP*AP*GP*TP*TP*CP*TP*T)-3'), ... (5 entities in total)
• 機能のキーワード: topoisomerase, asfv, inhibitor, viral protein, isomerase-dna complex, isomerase/dna
• 由来する生物種: African swine fever virus; 詳細
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 292424.89

構造登録者

Chang, C.-W.,Tsai, M.-D. (登録日: 2023-05-05, 公開日: 2024-02-07, 最終更新日: 2024-04-17)

主引用文献

Chang, C.M.,Wang, S.C.,Wang, C.H.,Pang, A.H.,Yang, C.H.,Chang, Y.K.,Wu, W.J.,Tsai, M.D.
A unified view on enzyme catalysis by cryo-EM study of a DNA topoisomerase.
Commun Chem, 7:45-45, 2024

PubMed Abstract: 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.

PubMed: 38418525
DOI: 10.1038/s42004-024-01129-y

実験手法

ELECTRON MICROSCOPY (2.76 Å)