X-ray and biochemical anatomy of an archaeal XPF/Rad1/Mus81 family nuclease: similarity between its endonuclease domain and restriction enzymes

Structure. 2003 Apr;11(4):445-57. doi: 10.1016/s0969-2126(03)00046-7.


The XPF/Rad1/Mus81-dependent nuclease family specifically cleaves branched structures generated during DNA repair, replication, and recombination, and is essential for maintaining genome stability. Here, we report the domain organization of an archaeal homolog (Hef) of this family and the X-ray crystal structure of the middle domain, with the nuclease activity. The nuclease domain architecture exhibits remarkable similarity to those of restriction endonucleases, including the correspondence of the GDX(n)ERKX(3)D signature motif in Hef to the PDX(n)(E/D)XK motif in restriction enzymes. This structural study also suggests that the XPF/Rad1/Mus81/ERCC1 proteins form a dimer through each interface of the nuclease domain and the helix-hairpin-helix domain. Simultaneous disruptions of both interfaces result in their dissociation into separate monomers, with strikingly reduced endonuclease activities.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Archaeal Proteins / chemistry*
  • Archaeal Proteins / genetics
  • Archaeal Proteins / metabolism
  • Binding Sites
  • Crystallography, X-Ray
  • DNA Restriction Enzymes / chemistry
  • DNA Restriction Enzymes / genetics
  • DNA Restriction Enzymes / metabolism
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Dimerization
  • Endonucleases / chemistry*
  • Endonucleases / genetics
  • Endonucleases / metabolism
  • Humans
  • Metals / metabolism
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Conformation*
  • Sequence Alignment


  • Archaeal Proteins
  • DNA-Binding Proteins
  • Metals
  • xeroderma pigmentosum group F protein
  • Endonucleases
  • MUS81 protein, human
  • DNA Restriction Enzymes

Associated data

  • PDB/1J22
  • PDB/1J23
  • PDB/1J24