5WN3

APE1 F266A exonuclease substrate complex with a C/T mismatch

5WN3 の概要

• エントリーDOI: 10.2210/pdb5wn3/pdb
• 分子名称: DNA (5'-D(P*TP*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DV3))-3'), DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... (9 entities in total)
• 機能のキーワード: hydrolase, lyase-dna complex, lyase/dna
• 由来する生物種: Homo sapiens (Human); 詳細
• タンパク質・核酸の鎖数: 5
• 化学式量合計: 75424.39

構造登録者

Freudenthal, B.D.,Whitaker, A.M. (登録日: 2017-07-31, 公開日: 2018-02-28, 最終更新日: 2023-10-04)

主引用文献

Whitaker, A.M.,Flynn, T.S.,Freudenthal, B.D.
Molecular snapshots of APE1 proofreading mismatches and removing DNA damage.
Nat Commun, 9:399-399, 2018

PubMed Abstract: Human apurinic/apyrimidinic (AP) endonuclease 1 (APE1) is an essential DNA repair enzyme which uses a single active site to process DNA damage via two distinct activities: (1) AP-endonuclease and (2) 3' to 5' exonuclease. The AP-endonuclease activity cleaves at AP-sites, while the exonuclease activity excises bulkier 3' mismatches and DNA damage to generate clean DNA ends suitable for downstream repair. Molecular details of the exonuclease reaction and how one active site can accommodate various toxic DNA repair intermediates remains elusive despite being biologically important. Here, we report multiple high-resolution APE1-DNA structural snapshots revealing how APE1 removes 3' mismatches and DNA damage by placing the 3' group within the intra-helical DNA cavity via a non-base flipping mechanism. This process is facilitated by a DNA nick, instability of a mismatched/damaged base, and bending of the DNA. These results illustrate how APE1 cleanses DNA dirty-ends to generate suitable substrates for downstream repair enzymes.

PubMed: 29374164
DOI: 10.1038/s41467-017-02175-y

実験手法

X-RAY DIFFRACTION (2 Å)