7Z5A

Crystal structure of the trapped complex of mouse Endonuclease VIII-LIKE 3 (mNEIL3) and hairpin DNA with 5'overhang

Summary for 7Z5A

• Entry DOI: 10.2210/pdb7z5a/pdb
• Descriptor: Endonuclease 8-like 3, DNA (5'-D(P*TP*TP*TP*(PED)P*AP*CP*GP*CP*GP*AP*AP*GP*CP*GP*TP*G)-3'), ZINC ION, ... (4 entities in total)
• Functional Keywords: ap-icl, dna crosslink repair, neil3, ber, dna binding protein
• Biological source: Mus musculus (house mouse); More
• Total number of polymer chains: 2
• Total formula weight: 39364.81

Authors

Silhan, J.,Huskova, A. (deposition date: 2022-03-08, release date: 2022-10-19, Last modification date: 2024-01-31)

Primary citation

Huskova, A.,Dinesh, D.C.,Srb, P.,Boura, E.,Veverka, V.,Silhan, J.
Model of abasic site DNA cross-link repair; from the architecture of NEIL3 DNA binding domains to the X-structure model.
Nucleic Acids Res., 50:10436-10448, 2022

PubMed Abstract: Covalent DNA interstrand crosslinks are toxic DNA damage lesions that block the replication machinery that can cause a genomic instability. Ubiquitous abasic DNA sites are particularly susceptible to spontaneous cross-linking with a base from the opposite DNA strand. Detection of a crosslink induces the DNA helicase ubiquitination that recruits NEIL3, a DNA glycosylase responsible for the lesion removal. NEIL3 utilizes several zinc finger domains indispensable for its catalytic NEI domain repairing activity. They recruit NEIL3 to the repair site and bind the single-stranded DNA. However, the molecular mechanism underlying their roles in the repair process is unknown. Here, we report the structure of the tandem zinc-finger GRF domain of NEIL3 and reveal the molecular details of its interaction with DNA. Our biochemical data indicate the preferential binding of the GRF domain to the replication fork. In addition, we obtained a structure for the catalytic NEI domain in complex with the DNA reaction intermediate that allowed us to construct and validate a model for the interplay between the NEI and GRF domains in the recognition of an interstrand cross-link. Our results suggest a mechanism for recognition of the DNA replication X-structure by NEIL3, a key step in the interstrand cross-link repair.

PubMed: 36155818
DOI: 10.1093/nar/gkac793

Experimental method

X-RAY DIFFRACTION (2.28 Å)