HNH endonucleases cleave phosphodiester bonds in many biological contexts, including intron homing, degradation and repair of genomic DNA, and restriction of viral DNA (Goodrich-Blair and Shub 1996; Malik and Henikoff 2000; Bujnicki et al. 2001; James et al. 2002; San Filippo and Lambowitz 2002; Walker et al. 2002). In the 10 years since the HNH motif was first reported by Shub et al. (1994) and Gorbalenya (1994), around 500 members have been identified, which have the following database identifiers: cd00085, SM00507 and pfam01844. HNH enzymes are found in all biological kingdoms, encoded by group I and group II introns, inteins, as well as free-standing open reading frames (Dalgaard et al. 1997).

In the first part of this chapter (Sect. 2), we describe the consensus sequence subsets that are associated with HNH enzymes and the proteins that accommodate them. We then present the biochemical properties of HNH enzymes as a group (Sect. 3), and finally describe recent structural data on HNH enzymes bound to DNA highlighting plausible cleavage mechanisms (Sect. 4). Throughout, we describe how HNH enzymes are part of a wider group of enzymes generally referred to as P0a-Me or His-Me endonucleases that also includes His-Cys homing endonucleases (Galburt and Jurica, this Vol.) and the eukaryotic apoptotic enzyme caspase-activated DNase (CAD).

A.H. Keeble, M.J. Maté, C. Kleanthous (e-mail: [email protected]) Department of Biology, Area 10, University of York, Heslington YOlO 5YW, UK

Nucleic Acids and Molecular Biology, Vol. 16 Marlene Belfort et al. (Eds.) Homing Endonucleases and Inteins © Springer-Verlag Berlin Heidelberg 2005

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