The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif

EMBO J. 2007 May 2;26(9):2432-42. doi: 10.1038/sj.emboj.7601672. Epub 2007 Apr 5.


The homing endonuclease I-Ssp6803I causes the insertion of a group I intron into a bacterial tRNA gene-the only example of an invasive mobile intron within a bacterial genome. Using a computational fold prediction, mutagenic screen and crystal structure determination, we demonstrate that this protein is a tetrameric PD-(D/E)-XK endonuclease - a fold normally used to protect a bacterial genome from invading DNA through the action of restriction endonucleases. I-Ssp6803I uses its tetrameric assembly to promote recognition of a single long target site, whereas restriction endonuclease tetramers facilitate cooperative binding and cleavage of two short sites. The limited use of the PD-(D/E)-XK nucleases by mobile introns stands in contrast to their frequent use of LAGLIDADG and HNH endonucleases - which in turn, are rarely incorporated into restriction/modification systems.

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Bacterial Proteins / chemistry*
  • Base Sequence
  • Binding Sites
  • Computer Simulation
  • Crystallography, X-Ray
  • Deoxyribonuclease I / chemistry*
  • Introns
  • Models, Molecular*
  • Molecular Sequence Data
  • Protein Folding*
  • Protein Structure, Quaternary


  • Bacterial Proteins
  • Deoxyribonuclease I

Associated data

  • PDB/2OST