- EMDB-17816: Pyrococcus abyssi DNA polymerase D (PolD) in its editing mode bou... -
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基本情報
登録情報
データベース: EMDB / ID: EMD-17816
タイトル
Pyrococcus abyssi DNA polymerase D (PolD) in its editing mode bound to a primer/template substrate containing three consecutive mismatches
マップデータ
試料
複合体: Binary complex of PolD bound to PCNA and a primer/template duplex containing three consecutive mismatches
タンパク質・ペプチド: DNA polymerase II small subunit
タンパク質・ペプチド: DP2
タンパク質・ペプチド: DNA polymerase sliding clampDNAクランプ
DNA: 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: DNA (5'-D(P*AP*GP*CP*AP*CP*GP*GP*CP*TP*CP*GP*GP*CP*CP*CP*GP*G)-3')
リガンド: MAGNESIUM ION
リガンド: ZINC ION
キーワード
Polymerase (ポリメラーゼ) / DNA (デオキシリボ核酸) / Replication (DNA複製) / PolD / Archaea (古細菌) / Editing (編集) / Proofreading (校正) / Exonuclease (エキソヌクレアーゼ) / Nuclease (ヌクレアーゼ) / DNA BINDING PROTEIN (DNA結合タンパク質)
機能・相同性
機能・相同性情報
エキソデオキシリボヌクレアーゼI / single-stranded DNA 3'-5' DNA exonuclease activity / DNA catabolic process / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / DNAミスマッチ修復 / DNA修復 / DNA-templated DNA replication / DNAポリメラーゼ ...エキソデオキシリボヌクレアーゼI / single-stranded DNA 3'-5' DNA exonuclease activity / DNA catabolic process / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / DNAミスマッチ修復 / DNA修復 / DNA-templated DNA replication / DNAポリメラーゼ / DNA-directed DNA polymerase activity / DNA binding 類似検索 - 分子機能
ジャーナル: Nat Commun / 年: 2023 タイトル: Molecular basis for proofreading by the unique exonuclease domain of Family-D DNA polymerases. 著者: Leonardo Betancurt-Anzola / Markel Martínez-Carranza / Marc Delarue / Kelly M Zatopek / Andrew F Gardner / Ludovic Sauguet / 要旨: 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. ...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.