Arabidopsis AP endonuclease ARP complex with 20bp THF-containing DNA

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 

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This is version 1.3 of the entry. See complete history


Structural insights into the catalytic mechanism of the AP endonuclease AtARP.

Guo, W.Wu, W.Wen, Y.Gao, Y.Zhuang, S.Meng, C.Chen, H.Zhao, Z.Hu, K.Wu, B.

(2024) Structure 32: 780-794.e5

  • DOI: https://doi.org/10.1016/j.str.2024.02.014
  • Primary Citation of Related Structures:  
    8KA3, 8KA4, 8KA5

  • PubMed Abstract: 

    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.

  • Organizational Affiliation

    Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-(apurinic or apyrimidinic site) endonuclease, chloroplastic297Arabidopsis thalianaMutation(s): 0 
Gene Names: ARPREFAt2g41460T26J13.5
Find proteins for P45951 (Arabidopsis thaliana)
Explore P45951 
Go to UniProtKB:  P45951
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45951
Sequence Annotations
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (43-MER)
B, C, D
43synthetic construct
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3DR (Subject of Investigation/LOI)
Query on 3DR

Download Ideal Coordinates CCD File 
C5 H11 O6 P
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.093α = 90
b = 72.093β = 90
c = 188.189γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-21
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Database references, Structure summary
  • Version 1.2: 2024-04-03
    Changes: Database references
  • Version 1.3: 2024-06-19
    Changes: Database references