Mechanistic insight into the assembly of the HerA-NurA helicase-nuclease DNA end resection complex

Nucleic Acids Res. 2017 Nov 16;45(20):12025-12038. doi: 10.1093/nar/gkx890.


The HerA-NurA helicase-nuclease complex cooperates with Mre11 and Rad50 to coordinate the repair of double-stranded DNA breaks. Little is known, however, about the assembly mechanism and activation of the HerA-NurA. By combining hybrid mass spectrometry with cryo-EM, computational and biochemical data, we investigate the oligomeric formation of HerA and detail the mechanism of nucleotide binding to the HerA-NurA complex from thermophilic archaea. We reveal that ATP-free HerA and HerA-DNA complexes predominantly exist in solution as a heptamer and act as a DNA loading intermediate. The binding of either NurA or ATP stabilizes the hexameric HerA, indicating that HerA-NurA is activated by substrates and complex assembly. To examine the role of ATP in DNA translocation and processing, we investigated how nucleotides interact with the HerA-NurA. We show that while the hexameric HerA binds six nucleotides in an 'all-or-none' fashion, HerA-NurA harbors a highly coordinated pairwise binding mechanism and enables the translocation and processing of double-stranded DNA. Using molecular dynamics simulations, we reveal novel inter-residue interactions between the external ATP and the internal DNA binding sites. Overall, here we propose a stepwise assembly mechanism detailing the synergistic activation of HerA-NurA by ATP, which allows efficient processing of double-stranded DNA.

MeSH terms

  • Adenosine Triphosphate / chemistry
  • Adenosine Triphosphate / metabolism
  • Archaeal Proteins / chemistry
  • Archaeal Proteins / genetics
  • Archaeal Proteins / metabolism*
  • Binding Sites / genetics
  • DNA Breaks, Double-Stranded
  • DNA Helicases / chemistry
  • DNA Helicases / genetics
  • DNA Helicases / metabolism*
  • DNA Repair
  • DNA, Archaeal / chemistry
  • DNA, Archaeal / genetics
  • DNA, Archaeal / metabolism*
  • Deoxyribonucleases / chemistry
  • Deoxyribonucleases / genetics
  • Deoxyribonucleases / metabolism*
  • Models, Molecular
  • Nucleic Acid Conformation
  • Protein Binding
  • Protein Domains
  • Protein Multimerization
  • Sulfolobus solfataricus / enzymology
  • Sulfolobus solfataricus / genetics
  • Sulfolobus solfataricus / metabolism


  • Archaeal Proteins
  • DNA, Archaeal
  • Adenosine Triphosphate
  • Deoxyribonucleases
  • DNA Helicases