7N3Y image
Entry Detail
PDB ID:
7N3Y
Keywords:
HYDROLASE/DNA
Title:
Crystal Structure of Saccharomyces cerevisiae Apn2 Catalytic Domain E59Q/D222N Mutant in Complex with DNA
Biological Source:
Source Organism:
Saccharomyces cerevisiae, synthetic construct
Host Organism:
Escherichia coli
PDB Version:
Deposition Date:
2021-06-02
Release Date:
2022-09-28
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.73 Å
R-Value Free:
0.22
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 1 21 1
7N3Y validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Description:DNA-(apurinic or apyrimidinic site) endonuclease 2
Mutations:E59Q,D222N
Chain IDs:A, B, C, D
Chain Length:413
Number of Molecules:4
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38207 Pfam ID:PF03372
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(*TP*CP*CP*GP*AP*AP*AP*TP*(PST)P*(PST)P*(SC)P*(GS)P*(GS))-3')
Chain IDs:E, F, G
Chain Length:13
Number of Molecules:3
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(*CP*CP*GP*AP*AP*AP*TP*TP*(PST)P*(SC)P*(GS)P*(GS)P*(AS))-3')
Chain IDs:H
Chain Length:13
Number of Molecules:1
Biological Source:synthetic construct
Ligand Molecules
CA
CIT
EDO
TAR
TLA
Primary Citation
Molecular basis for processing of topoisomerase 1-triggered DNA damage by Apn2/APE2.
Cell Rep 41 111448 111448 (2022)
PMID: 36198268 DOI: 10.1016/j.celrep.2022.111448

Abstact

Topoisomerase 1 (Top1) incises DNA containing ribonucleotides to generate complex DNA lesions that are resolved by APE2 (Apn2 in yeast). How Apn2 engages and processes this DNA damage is unclear. Here, we report X-ray crystal structures and biochemical analysis of Apn2-DNA complexes to demonstrate how Apn2 frays and cleaves 3' DNA termini via a wedging mechanism that facilitates 1-6 nucleotide endonucleolytic cleavages. APN2 deletion and DNA-wedge mutant Saccharomyces cerevisiae strains display mutator phenotypes, cell growth defects, and sensitivity to genotoxic stress in a ribonucleotide excision repair (RER)-defective background harboring a high density of Top1-incised ribonucleotides. Our data implicate a wedge-and-cut mechanism underpinning the broad-specificity Apn2 nuclease activity that mitigates mutagenic and genome instability phenotypes caused by Top1 incision at genomic ribonucleotides incorporated by DNA polymerase epsilon.

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Disease

Primary Citation of related structures
7N3Z