Type II restriction endonuclease R.Hpy188I belongs to the GIY-YIG nuclease superfamily,but exhibits an unusual active site |
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| Authors: | Katarzyna H Kaminska Mikihiko Kawai Michal Boniecki Ichizo Kobayashi Janusz M Bujnicki |
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| Affiliation: | (1) Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02-109 Warsaw, Poland;(2) Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland;(3) Department of Medical Genome Sciences, Graduate School of Frontier Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku Tokyo, 108-8639, Japan;(4) Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku Tokyo, 108-8639, Japan |
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| Abstract: | Background Catalytic domains of Type II restriction endonucleases (REases) belong to a few unrelated three-dimensional folds. While the PD-(D/E)XK fold is most common among these enzymes, crystal structures have been also determined for single representatives of two other folds: PLD (R.BfiI) and half-pipe (R.PabI). Bioinformatics analyses supported by mutagenesis experiments suggested that some REases belong to the HNH fold (e.g. R.KpnI), and that a small group represented by R.Eco29kI belongs to the GIY-YIG fold. However, for a large fraction of REases with known sequences, the three-dimensional fold and the architecture of the active site remain unknown, mostly due to extreme sequence divergence that hampers detection of homology to enzymes with known folds. |
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