Structure of the hexameric HerA ATPase reveals a mechanism of translocation-coupled DNA-end processing in archaea

Nat Commun. 2014 Nov 25:5:5506. doi: 10.1038/ncomms6506.

Abstract

The HerA ATPase cooperates with the NurA nuclease and the Mre11-Rad50 complex for the repair of double-strand DNA breaks in thermophilic archaea. Here we extend our structural knowledge of this minimal end-resection apparatus by presenting the first crystal structure of hexameric HerA. The full-length structure visualizes at atomic resolution the N-terminal HerA-ATP synthase domain and a conserved C-terminal extension, which acts as a physical brace between adjacent protomers. The brace also interacts in trans with nucleotide-binding residues of the neighbouring subunit. Our observations support a model in which the coaxial interaction of the HerA ring with the toroidal NurA dimer generates a continuous channel traversing the complex. HerA-driven translocation would propel the DNA towards the narrow annulus of NurA, leading to duplex melting and nucleolytic digestion. This system differs substantially from the bacterial end-resection paradigms. Our findings suggest a novel mode of DNA-end processing by this integrated archaeal helicase-nuclease machine.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphatases / chemistry*
  • Adenosine Triphosphatases / genetics
  • Adenosine Triphosphatases / metabolism*
  • Amino Acid Sequence
  • Archaea / chemistry
  • Archaea / enzymology*
  • Archaea / genetics
  • Archaeal Proteins / chemistry
  • Archaeal Proteins / genetics
  • Archaeal Proteins / metabolism*
  • DNA Breaks, Double-Stranded
  • DNA, Archaeal / genetics*
  • DNA, Archaeal / metabolism
  • Deoxyribonucleases / genetics
  • Deoxyribonucleases / metabolism
  • Models, Molecular
  • Molecular Sequence Data
  • Sequence Alignment
  • Translocation, Genetic*

Substances

  • Archaeal Proteins
  • DNA, Archaeal
  • Deoxyribonucleases
  • Adenosine Triphosphatases

Associated data

  • PDB/4D2I