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| Subject Categories: Microbiology & Pathogens | Structural Biology |
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| The EMBO Journal
(2007) 26, 2432–2442, doi:10.1038/sj.emboj.7601672 Published online 5 April 2007 |
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| The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif |
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| Lei Zhao1, 2, Richard P Bonocora3, 4, David A Shub3 and Barry L Stoddard2 |
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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 To whom correspondence should be addressed 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 4 Present 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; Published online 5 April 2007. |
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| Abstract |
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| 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. |
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| Keywords: group I intron, homing endonuclease, PD-(D/E)-XK fold, protein–DNA binding, restriction endonuclease |
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