DOE OSTI · 3030789
EEPD1 evolved a unique DNA clamping dimer protecting reversed replication forks
Abstract
Exonuclease/endonuclease/phosphatase (EEP)-fold hydrolases are canonically monomeric phosphodiesterases exemplified by APE1, DNase I, and TDP2 nucleases. While EEP family domain containing protein 1 (EEPD1) acts in DNA stress responses, its proposed nuclease activities are enigmatic. Here, we integrate hybrid structural methods, evolution, biochemistry, cancer genomics, plus molecular and cell biology to define EEPD1 structure, assembly, and function at stalled DNA replication forks. Results imply EEPD1 surprisingly requires both unique EEP domain dimer and distinctive tandem Helix-hairpin-Helix [(HhH) 2 ] domains to clamp double-stranded (ds) DNA at reversed DNA replication forks for fork protection. Small-angle X-ray Scattering (SAXS), crystal, and cryo-EM structures unveil an unprecedented tryptophan handshake dimer, conserved interface di-Trp-Pro pocket, and adjustable “wrist” enabling an open-closed conformational switch. EEPD1 dimer cooperatively binds complex dsDNA replication fork intermediates but alone lacks nuclease activity due to loss of key EEP catalytic residues during Metazoan evolution and atmospheric oxygen buildup. Instead, EEPD1 prevents nucleolytic degradation of reversed replication forks by MRE11. Furthermore, cancer bioinformatics support oxidative damage-dependent EEPD1 association as a significant modulator of overall patient survival. Collective findings uncover unexpected EEP dimer and fork protection function in clamping, not cleaving, reversed replication forks for metazoan oxidative stress responses controlling genome stability and cancer outcomes.
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Shen, Runze [Univ. of Texas, Houston, TX (United States). MD Anderson Cancer Center], Sarker, Altaf H. [Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)], Chen, Yue [Univ. of Texas, Houston, TX (United States). MD Anderson Cancer Center], Liu, Min [Univ. of Texas, Houston, TX (United States). MD Anderson Cancer Center], Roy, Sunetra [Univ. of Texas, Houston, TX (United States). MD Anderson Cancer Center], Arvai, Andrew S. [The Scripps Research Inst., La Jolla, CA (United States)], Bacolla, Albino [Univ. of Texas, Houston, TX (United States). MD Anderson Cancer Center] (ORCID:0000000302068423), Ahmed, Zamal [Univ. of Texas, Houston, TX (United States). MD Anderson Cancer Center], Katsonis, Panagiotis [Baylor College of Medicine, Houston, TX (United States)], Hammel, Michal [Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)], Kuraoka, Isao [Fukuoka Univ. (Japan)] (ORCID:0000000163913411), Tsai, Miaw-Sheue [Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)], Irie, Corydon [Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)], Webb, Lukas [Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)] (ORCID:0009000056321637), Lichtarge, Olivier [Baylor College of Medicine, Houston, TX (United States)], Tsai, Chi-Lin [Univ. of Texas, Houston, TX (United States). MD Anderson Cancer Center], Tsutakawa, Susan E. [Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)] (ORCID:0000000249184571), Schlacher, Katharina [Univ. of Texas, Houston, TX (United States). MD Anderson Cancer Center], Tainer, John A. [Univ. of Texas, Houston, TX (United States). MD Anderson Cancer Center; Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)] (ORCID:0000000316592429). 2026-03-14. EEPD1 evolved a unique DNA clamping dimer protecting reversed replication forks. https://doi.org/10.1093/nar%2Fgkag188
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