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Nucleic Acids Research, 2002, Vol. 30, No. 18 3962-3971
© 2002 Oxford University Press

High resolution crystal structure of domain I of the Saccharomyces cerevisiae homing endonuclease PI-SceI

Erik Werner1, Wolfgang Wende2, Alfred Pingoud2 and Udo Heinemann*,1,3

1 Crystallography Group, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13092 Berlin, Germany, 2 Institute of Biochemistry, Justus Liebig University, Heinrich-Buff-Ring 58, 35392 Gießen, Germany and 3 Institute of Chemistry–Crystallography, Free University of Berlin, Takustraße 6, 14195 Berlin, Germany

*To whom correspondence should be addressed at: Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13092 Berlin, Germany. Tel: +49 30 9406 3420; Fax: +49 30 9406 2548; Email: heinemann{at}mdc-berlin.de

The homing endonuclease PI-SceI from Saccharo myces cerevisiae consists of two domains. The protein splicing domain I catalyzes the excision of the mature endonuclease (intein) from a precursor protein and the religation of the flanking amino acid sequences (exteins) to a functional protein. Furthermore, domain I is involved in binding and recognition of the specific DNA substrate. Domain II of PI-SceI, the endonuclease domain, which is structurally homologous to other homing endonucleases from the LAGLIDADG family, harbors the endonucleolytic center of PI-SceI, which in vivo initiates the homing process by introducing a double-strand cut in the ~35 bp recognition sequence. At 1.35 Å resolution, the crystal structure of PI-SceI domain I provides a detailed view of the part of the protein that is responsible for tight and specific DNA binding. A geometry-based docking of the 75° bent recognition sequence to the full-length protein implies a conformational change or hinge movement of a subdomain of domain I, the tongs part, that is predicted to reach into the major groove near base pairs +16 to +18.


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