9X1P

The cryo-EM structure of HerA-NurA complex with ATPgammaS and dsDNA from Thermococcus kodakarensis (State 3)

Summary for 9X1P

• Entry DOI: 10.2210/pdb9x1p/pdb
• EMDB information: 66466
• Descriptor: DNA helicase, 5'-3' nuclease, encoded next to Rad50 and Mre11 homologs, DNA, ... (7 entities in total)
• Functional Keywords: hera, helicase, nura, nuclease, dna binding protein
• Biological source: Thermococcus kodakarensis; More
• Total number of polymer chains: 10
• Total formula weight: 509754.34

Authors

Uda, K.,Numata, T. (deposition date: 2025-10-02, release date: 2026-02-04, Last modification date: 2026-04-29)

Primary citation

Uda, K.,Yamagami, T.,Ishino, S.,Gerle, C.,Gopalasingam, C.C.,Shigematsu, H.,Numata, T.,Ishino, Y.
Substrate specificity and action mechanism of the HerA-NurA nuclease from the hyperthermophilic archaeon Thermococcus kodakarensis.
Mbio, 17:e0352325-e0352325, 2026

PubMed Abstract: The HerA-NurA complex reportedly functions in DNA end resection in archaea. End resection is important to start homologous recombination by forming a single-stranded DNA region with an overhanging 3'-end, which invades double-stranded DNA (dsDNA) with a homologous sequence to form a D-loop. Here, we studied the structure and functions of HerA-NurA from the hyperthermophilic archaeon, . Our analyses demonstrated that NurA is a non-directional and single-stranded specific nuclease, but the HerA-NurA complex cleaves both strands of dsDNA in an exonucleolytic manner, regardless of the structure of the DNA end. The 3D structures of HerA-NurA and its complex with dsDNA revealed the detailed molecular mechanisms of these nuclease reactions. These results suggest that HerA-NurA may not be involved in the end resection process but instead performs other functions, such as exerting an antiviral function by degrading the dsDNA of foreign viruses, similar to recent studies in bacteria.

PubMed: 41641993
DOI: 10.1128/mbio.03523-25

Experimental method

ELECTRON MICROSCOPY (3.1 Å)