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  • The EMBO Journal (2007) 26, 2432 - 2442
  • doi:10.1038/sj.emboj.7601672

Published online: 5 April 2007

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

Lei Zhao1,2, Richard P Bonocora3,a, David A Shub3 and Barry L Stoddard2

  1. Graduate Program in Molecular Biophysics, Structure and Design, University of Washington, Seattle, WA, USA
  2. Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle WA, USA
  3. Department of Biological Sciences and Center for Molecular Genetics, University at Albany, State University of New York, Albany, NY, USA

Correspondence to:

Barry L Stoddard, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N. A3-025, Seattle, WA 98109, USA. Tel.: +1 206 667 4031; Fax: +1 206 667 3331; E-mail: bstoddar@fhcrc.org

aPresent address: Gene Expression and Regulation Section, Laboratory of Molecular and Cellular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892-0830 USA

Received 8 February 2007; Accepted 9 March 2007

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.

  • Keywords:

    • group I intron,
    • homing endonuclease,
    • PD-(D/E)-XK fold,
    • protein–DNA binding,
    • restriction endonuclease