8PPU

Pyrococcus abyssi DNA polymerase D (PolD) in its editing mode bound to a primer/template substrate containing three consecutive mismatches

8PPU の概要

• エントリーDOI: 10.2210/pdb8ppu/pdb
• EMDBエントリー: 17816
• 分子名称: DNA (5'-D(P*CP*CP*GP*GP*GP*CP*CP*GP*AP*GP*CP*CP*GP*TP*(GS)P*(C7R)P*(PST)P*(PST)P*(PST))-3'), DNA (5'-D(P*AP*GP*CP*AP*CP*GP*GP*CP*TP*CP*GP*GP*CP*CP*CP*GP*G)-3'), DNA polymerase II small subunit, ... (7 entities in total)
• 機能のキーワード: polymerase, dna, replication, pold, archaea, editing, proofreading, exonuclease, nuclease, dna binding protein
• 由来する生物種: Pyrococcus abyssi GE5; 詳細
• タンパク質・核酸の鎖数: 7
• 化学式量合計: 321343.53

構造登録者

Betancurt-Anzola, L.,Martinez-Carranza, M.,Zatopek, K.M.,Gardner, A.F.,Sauguet, L. (登録日: 2023-07-10, 公開日: 2023-12-20, 最終更新日: 2024-11-13)

主引用文献

Betancurt-Anzola, L.,Martinez-Carranza, M.,Delarue, M.,Zatopek, K.M.,Gardner, A.F.,Sauguet, L.
Molecular basis for proofreading by the unique exonuclease domain of Family-D DNA polymerases.
Nat Commun, 14:8306-8306, 2023

PubMed Abstract: Replicative DNA polymerases duplicate entire genomes at high fidelity. This feature is shared among the three domains of life and is facilitated by their dual polymerase and exonuclease activities. Family D replicative DNA polymerases (PolD), found exclusively in Archaea, contain an unusual RNA polymerase-like catalytic core, and a unique Mre11-like proofreading active site. Here, we present cryo-EM structures of PolD trapped in a proofreading mode, revealing an unanticipated correction mechanism that extends the repertoire of protein domains known to be involved in DNA proofreading. Based on our experimental structures, mutants of PolD were designed and their contribution to mismatch bypass and exonuclease kinetics was determined. This study sheds light on the convergent evolution of structurally distinct families of DNA polymerases, and the domain acquisition and exchange mechanism that occurred during the evolution of the replisome in the three domains of life.

PubMed: 38097591
DOI: 10.1038/s41467-023-44125-x

実験手法

ELECTRON MICROSCOPY (3.02 Å)