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

• Published in: Nucleic acids research Vol. 39; no. 2; pp. 712 - 719
• Main Authors: Vanamee, Éva Scheuring, Viadiu, Hector, Chan, Siu-Hong, Ummat, Ajay, Hartline, Adrian M, Xu, Shuang-yong, Aggarwal, Aneel K
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.01.2011
• Subjects: 60 APPLIED LIFE SCIENCES; Amino Acid Sequence; ASYMMETRY; BASIC BIOLOGICAL SCIENCES; Catalytic Domain; Deoxyribonuclease BamHI - chemistry; Deoxyribonucleases, Type II Site-Specific - chemistry; Deoxyribonucleases, Type II Site-Specific - metabolism; DNA; DNA - chemistry; Endonuclease; ENZYMES; Homology; Models, Molecular; Molecular Sequence Data; Nucleic Acid Conformation; Nucleotide sequence; Protein Binding; Sequence Homology, Amino Acid; Structural Biology; Substrate Specificity
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkq779

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.