Journal Article

Asymmetric DNA recognition by the OkrAI endonuclease, an isoschizomer of BamHI

Éva Scheuring Vanamee, Hector Viadiu, Siu-Hong Chan, Ajay Ummat, Adrian M. Hartline, Shuang-yong Xu and Aneel K. Aggarwal

in Nucleic Acids Research

Volume 39, issue 2, pages 712-719
Published in print January 2011 | ISSN: 0305-1048
Published online September 2010 | e-ISSN: 1362-4962 | DOI: http://dx.doi.org/10.1093/nar/gkq779

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Restriction enzymes share little or no sequence homology with the exception of isoschizomers, or enzymes that recognize and cleave the same DNA sequence. We present here the structure of a BamHI isoschizomer, OkrAI, bound to the same DNA sequence (TATGGATCCATA) as that cocrystallized with BamHI. We show that OkrAI is a more minimal version of BamHI, lacking not only the N- and C-terminal helices but also an internal 310 helix and containing β-strands that are shorter than those in BamHI. Despite these structural differences, OkrAI recognizes the DNA in a remarkably similar manner to BamHI, including asymmetric contacts via C-terminal ‘arms’ that appear to ‘compete’ for the minor groove. However, the arms are shorter than in BamHI. We observe similar DNA-binding affinities between OkrAI and BamHI but OkrAI has higher star activity (at 37°C) compared to BamHI. Together, the OkrAI and BamHI structures offer a rare opportunity to compare two restriction enzymes that work on exactly the same DNA substrate.

Journal Article.  4279 words.  Illustrated.

Subjects: Chemistry ; Biochemistry ; Bioinformatics and Computational Biology ; Genetics and Genomics ; Molecular and Cell Biology

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