title: The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif.
abstract: 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.
authors.affiliation: Graduate Program in Molecular Biophysics, Structure and Design, University of Washington, Seattle, WA, USA.
authors.forename: Lei
authors.initials: L
authors.lastname: Zhao
authors.forename: Richard P
authors.initials: RP
authors.lastname: Bonocora
authors.forename: David A
authors.initials: DA
authors.lastname: Shub
authors.forename: Barry L
authors.initials: BL
authors.lastname: Stoddard
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D001483:Base Sequence; D001665:Binding Sites; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D003850:Deoxyribonuclease I / Q000737:chemistry*; D007438:Introns; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017510:Protein Folding; D020836:Protein Structure, Quaternary
chemical_list: D001426:Bacterial Proteins; D003850:Deoxyribonuclease I