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A more recent version of this article appeared on February 11, 2005
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M409020200v1
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Papers In Press, published online ahead of print November 24, 2004
J. Biol. Chem, 10.1074/jbc.M409020200
Submitted on August 6, 2004
Revised on November 22, 2004
Accepted on November 24, 2004

Specificity changes in the evolution of type II restriction endonucleases: a biochemical and bioinformatic analysis of restriction enzymes that recognize unrelated sequences

Vera Pingoud, Anna Sudina, Hildegard Geyer, Janusz M. Bujnicki, Rudi Lurz, Gerhild Lüder, Richard Morgan, Elena Kubareva, and Alfred Pingoud

Institut für Biochemie, FB 08, Justus-Liebig-Universität Giessen, Giessen 35392

Corresponding Author: vera.pingoud{at}chemie.bio.uni-giessen.de

How restriction enzymes with their different specificities and mode of cleavage evolved has been a long standing question in evolutionary biology. We have recently shown that several Type II restriction endonucleases, viz. SsoII (/CCNGG), PspGI (/CCWGG), EcoRII (/CCWGG), NgoMIV (G/CCGGC) and Cfr10I (R/CCGGY), which recognize similar DNA sequences (as indicated, where slash denotes cleavage position), share limited sequence similarity over an interrupted stretch of ca. 70 amino acid residues with MboI, a Type II restriction endonuclease from Moraxella bovis (Pingoud et al. 2003, J. Mol. Biol. 329, 913-929). Nevertheless, MboI has a dissimilar DNA specificity (/GATC) compared to these enzymes. In this study, we characterize MboI in detail to determine whether it utilizes a mechanism of DNA recognition similar to SsoII, PspGI, EcoRII, NgoMIV and Cfr10I. Mutational analyses and photocross-linking experiments demonstrate that MboI exploits the ca. 70 amino acid stretch for DNA recognition and cleavage. It is therefore likely that MboI shares a common evolutionary origin with SsoII, PspGI, EcoRII, NgoMIV and Cfr10I. This is the first example of a relatively close evolutionary link between Type II restriction enzymes of widely different specificities.


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