7SUV

APE1 exonuclease substrate complex with 8oxoG opposite A

7SUV の概要

• エントリーDOI: 10.2210/pdb7suv/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*(8OG))-3'), DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... (5 entities in total)
• 機能のキーワード: nuclease, dna repair protein, dna binding protein, hydrolase, hydrolase-dna complex, hydrolase/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: 75193.38

構造登録者

Whitaker, A.W.,Freudenthal, B.D. (登録日: 2021-11-18, 公開日: 2022-09-07, 最終更新日: 2023-10-18)

主引用文献

Whitaker, A.M.,Stark, W.J.,Freudenthal, B.D.
Processing oxidatively damaged bases at DNA strand breaks by APE1.
Nucleic Acids Res., 50:9521-9533, 2022

PubMed Abstract: Reactive oxygen species attack the structure of DNA, thus altering its base-pairing properties. Consequently, oxidative stress-associated DNA lesions are a major source of the mutation load that gives rise to cancer and other diseases. Base excision repair (BER) is the pathway primarily tasked with repairing DNA base damage, with apurinic/apyrimidinic endonuclease (APE1) having both AP-endonuclease and 3' to 5' exonuclease (exo) DNA cleavage functions. The lesion 8-oxo-7,8-dihydroguanine (8-oxoG) can enter the genome as either a product of direct damage to the DNA, or through polymerase insertion at the 3'-end of a DNA strand during replication or repair. Importantly, 3'-8-oxoG impairs the ligation step of BER and therefore must be removed by the exo activity of a surrogate enzyme to prevent double stranded breaks and cell death. In the present study, we use X-ray crystallography to characterize the exo activity of APE1 on 3'-8-oxoG substrates. These structures support a unified APE1 exo mechanism that differs from its more canonical AP-endonuclease activity. In addition, through complementation of the structural data with enzyme kinetics and binding studies employing both wild-type and rationally designed APE1 mutants, we were able to identify and characterize unique protein: DNA contacts that specifically mediate 8-oxoG removal by APE1.

PubMed: 36018803
DOI: 10.1093/nar/gkac695

実験手法

X-RAY DIFFRACTION (1.99 Å)