Nucleic Acids Research Advance Access published online on October 1, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn622
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Structural Biology |
Central base pair flipping and discrimination by PspGI
1International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland, 2Max-Planck-Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01309 Dresden, Germany, 3Department of Chemistry, Wayne State University, Detroit, MI 48202, USA, 4Institute of Biotechnology, Graiciuno 8, LT-02241, Vilnius, Lithuania and 5Schools of Chemistry and Biosciences, Main Building, Park Place, Cardiff University, Cardiff CF10 3AT, UK
*To whom correspondence should be addressed. Tel: +48 22 5970732 (Warsaw); Tel: +44 29 208 70625 (Cardiff); Fax: +48 22 597 0715; Email: mbochtler{at}iimcb.gov.pl or bochtlerm{at}cardiff.ac.uk
Received July 28, 2008. Revised September 11, 2008. Accepted September 11, 2008.
PspGI is a representative of a group of restriction endonucleases that recognize a pentameric sequence related to CCNGG. Unlike the previously investigated Ecl18kI, which does not have any specificity for the central base pair, PspGI prefers A/T over G/C in its target site. Here, we present a structure of PspGI with target DNA at 1.7 Å resolution. In this structure, the bases at the center of the recognition sequence are extruded from the DNA and flipped into pockets of PspGI. The flipped thymine is in the usual anti conformation, but the flipped adenine takes the normally unfavorable syn conformation. The results of this and the accompanying manuscript attribute the preference for A/T pairs over G/C pairs in the flipping position to the intrinsically lower penalty for flipping A/T pairs and to selection of the PspGI pockets against guanine and cytosine. Our data show that flipping can contribute to the discrimination between normal bases. This adds a new role to base flipping in addition to its well-known function in base modification and DNA damage repair.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
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