8KA4 image
Entry Detail
PDB ID:
8KA4
Keywords:
Title:
Arabidopsis AP endonuclease ARP complex with 21bp THF-containing DNA
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2023-08-02
Release Date:
2024-02-21
Method Details:
Experimental Method:
Resolution:
2.30 Å
R-Value Free:
0.23
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:DNA-(apurinic or apyrimidinic site) endonuclease, chloroplastic
Chain IDs:A, B, C, D
Chain Length:297
Number of Molecules:4
Biological Source:Arabidopsis thaliana
Primary Citation
Structural insights into the catalytic mechanism of the AP endonuclease AtARP.
Structure 32 780 794.e5 (2024)
PMID: 38503293 DOI: 10.1016/j.str.2024.02.014

Abstact

Base excision repair (BER) is a critical genome defense pathway that copes with a broad range of DNA lesions induced by endogenous or exogenous genotoxic agents. AP endonucleases in the BER pathway are responsible for removing the damaged bases and nicking the abasic sites. In plants, the BER pathway plays a critical role in the active demethylation of 5-methylcytosine (5mC) DNA modification. Here, we have determined the crystal structures of Arabidopsis AP endonuclease AtARP in complex with the double-stranded DNA containing tetrahydrofuran (THF) that mimics the abasic site. We identified the critical residues in AtARP for binding and removing the abasic site and the unique residues for interacting with the orphan base. Additionally, we investigated the differences among the three plant AP endonucleases and evaluated the general DNA repair capacity of AtARP in a mammalian cell line. Our studies provide further mechanistic insights into the BER pathway in plants.

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