Archaeal NurA nuclease: structure, catalytic mechanism, and functional cooperation in DNA double-strand break repair

Abstract DNA double-strand breaks (DSBs) are highly cytotoxic lesions that endanger genome stability. In archaea, NurA nuclease is a core component of minimal DNA end-resection system by working with HerA helicase and Mre11-Rad50 complex to produce 3′ single-stranded DNA tails for homologous recombination. NurA homologs exist in archaea and some bacteria, but not in eukaryotes. Widespread uncharacterized NurA homologs are distributed across the Asgard superphylum, and exploring these proteins provides critical evolutionary clues for tracing the gain and loss of conserved DSB repair machinery during the prokaryote-eukaryote transition. Archaeal NurA nuclease forms a toroidal dimer and possesses both 5′ → 3′ exonuclease and endonuclease activities. Divalent metal ions, especially Mn2⁺, are essential for archaeal NurA nuclease’s catalysis, and key amino acids responsible for DNA binding and cleavage have been identified. Additionally, archaeal NurA nuclease cooperates with HerA helicase to form a continuous channel for DNA processing. This review summarizes recent progress of archaeal NurA nuclease, focusing on its structure, enzymatic activities and mechanisms, evolutionary relationship, and interactions in DNA end-resection machinery. We further highlight major knowledge gaps in Asgard NurA research and propose future biochemical and structural characterization of these proteins to clarify ancient evolutionary trajectories of DSB repair pathways. These findings deepen our understanding of archaeal DSB repair and provide evolutionary clues for conserved DSB repair pathways across all life domains. Key points • Archaeal NurA nuclease functions as a Mn2⁺-dependent dimeric nuclease with dual enzymatic activities, and only euryarchaeal NurA possesses a specific M domain. • Archaeal NurA nuclease collaborates with HerA-Mre11-Rad50 to complete DSB end resection. • NurA nuclease is distributed in archaea including Asgard and certain bacteria but is missing in eukaryotes, and Asgard-derived NurA has not been characterized experimentally.