9YXY

Crystal structure of EEPD1 EEP domain dimer at pH 5.5

Summary for 9YXY

• Entry DOI: 10.2210/pdb9yxy/pdb
• Related: 9YI2 9YSF
• Descriptor: Endonuclease/exonuclease/phosphatase family domain-containing protein 1, GLYCEROL, 1,2-ETHANEDIOL, ... (5 entities in total)
• Functional Keywords: endonuclease/exonuclease/phosphatase fold, dimerization, replication stress response, dna binding protein
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 2
• Total formula weight: 66650.37

Authors

Shen, R.,Arvai, A.S.,Brosey, C.A.,Tsai, C.,Tsutakawa, S.E.,Tainer, J.A. (deposition date: 2025-10-27, release date: 2026-03-18, Last modification date: 2026-03-25)

Primary citation

Shen, R.,Sarker, A.H.,Chen, Y.,Liu, M.,Roy, S.,Arvai, A.S.,Bacolla, A.,Ahmed, Z.,Katsonis, P.,Hammel, M.,Kuraoka, I.,Tsai, M.S.,Irie, C.,Webb, L.,Lichtarge, O.,Tsai, C.L.,Tsutakawa, S.E.,Schlacher, K.,Tainer, J.A.
EEPD1 evolved a unique DNA clamping dimer protecting reversed replication forks.
Nucleic Acids Res., 54:-, 2026

PubMed 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.

PubMed: 41830330
DOI: 10.1093/nar/gkag188

Experimental method

X-RAY DIFFRACTION (2 Å)