8OOY

Pol I bound to extended and displaced DNA section - open conformation

8OOY の概要

• エントリーDOI: 10.2210/pdb8ooy/pdb
• EMDBエントリー: 17033
• 分子名称: DNA polymerase I, Template DNA, Extending Primer, ... (5 entities in total)
• 機能のキーワード: dna polymerase i, okazaki fragment maturation, dna binding protein
• 由来する生物種: Escherichia coli 'BL21-Gold(DE3)pLysS AG'; 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 84194.89

構造登録者

Botto, M.,Borsellini, A.,Lamers, M.H. (登録日: 2023-04-06, 公開日: 2023-08-09, 最終更新日: 2025-07-09)

主引用文献

Botto, M.M.,Borsellini, A.,Lamers, M.H.
A four-point molecular handover during Okazaki maturation.
Nat.Struct.Mol.Biol., 30:1505-1515, 2023

PubMed Abstract: DNA replication introduces thousands of RNA primers into the lagging strand that need to be removed for replication to be completed. In Escherichia coli when the replicative DNA polymerase Pol IIIα terminates at a previously synthesized RNA primer, DNA Pol I takes over and continues DNA synthesis while displacing the downstream RNA primer. The displaced primer is subsequently excised by an endonuclease, followed by the sealing of the nick by a DNA ligase. Yet how the sequential actions of Pol IIIα, Pol I polymerase, Pol I endonuclease and DNA ligase are coordinated is poorly defined. Here we show that each enzymatic activity prepares the DNA substrate for the next activity, creating an efficient four-point molecular handover. The cryogenic-electron microscopy structure of Pol I bound to a DNA substrate with both an upstream and downstream primer reveals how it displaces the primer in a manner analogous to the monomeric helicases. Moreover, we find that in addition to its flap-directed nuclease activity, the endonuclease domain of Pol I also specifically cuts at the RNA-DNA junction, thus marking the end of the RNA primer and creating a 5' end that is a suitable substrate for the ligase activity of LigA once all RNA has been removed.

PubMed: 37620586
DOI: 10.1038/s41594-023-01071-y

実験手法

ELECTRON MICROSCOPY (4 Å)