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Proc Natl Acad Sci U S A. 2017 Jan 10;114(2):304-309. doi: 10.1073/pnas.1610011114. Epub 2016 Dec 27.

APE2 Zf-GRF facilitates 3'-5' resection of DNA damage following oxidative stress.

Author information

1
Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709.
2
Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223.
3
Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223 shan.yan@uncc.edu williamsrs@niehs.nih.gov.
4
Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709 shan.yan@uncc.edu williamsrs@niehs.nih.gov.

Abstract

The Xenopus laevis APE2 (apurinic/apyrimidinic endonuclease 2) nuclease participates in 3'-5' nucleolytic resection of oxidative DNA damage and activation of the ATR-Chk1 DNA damage response (DDR) pathway via ill-defined mechanisms. Here we report that APE2 resection activity is regulated by DNA interactions in its Zf-GRF domain, a region sharing high homology with DDR proteins Topoisomerase 3α (TOP3α) and NEIL3 (Nei-like DNA glycosylase 3), as well as transcription and RNA regulatory proteins, such as TTF2 (transcription termination factor 2), TFIIS, and RPB9. Biochemical and NMR results establish the nucleic acid-binding activity of the Zf-GRF domain. Moreover, an APE2 Zf-GRF X-ray structure and small-angle X-ray scattering analyses show that the Zf-GRF fold is typified by a crescent-shaped ssDNA binding claw that is flexibly appended to an APE2 endonuclease/exonuclease/phosphatase (EEP) catalytic core. Structure-guided Zf-GRF mutations impact APE2 DNA binding and 3'-5' exonuclease processing, and also prevent efficient APE2-dependent RPA recruitment to damaged chromatin and activation of the ATR-Chk1 DDR pathway in response to oxidative stress in Xenopus egg extracts. Collectively, our data unveil the APE2 Zf-GRF domain as a nucleic acid interaction module in the regulation of a key single-strand break resection function of APE2, and also reveal topologic similarity of the Zf-GRF to the zinc ribbon domains of TFIIS and RPB9.

KEYWORDS:

APE2; Xenopus laevis; Zf-GRF; crystallography; oxidative stress

PMID:
28028224
PMCID:
PMC5240719
DOI:
10.1073/pnas.1610011114
[Indexed for MEDLINE]
Free PMC Article

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