SNAP output for PDB entry 7n3y [SNAP web server]

PDB-id

7n3y; SNAP-derived features in text and JSON formats; DNAproDB

Class

hydrolase-DNA

Method

X-ray (2.73 Å)

Summary

Crystal structure of saccharomyces cerevisiae apn2 catalytic domain e59q-d222n mutant in complex with DNA

Reference

Williams JS, Wojtaszek JL, Appel DC, Krahn J, Wallace BD, Walsh E, Kunkel TA, Williams RS (2022): "Molecular basis for processing of topoisomerase 1-triggered DNA damage by Apn2/APE2." Cell Rep, 41, 111448. doi: 10.1016/j.celrep.2022.111448.

Abstract

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.