title: Asymmetric DNA recognition by the OkrAI endonuclease, an isoschizomer of BamHI.
abstract: 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 3(10) 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.
authors.affiliation: Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, NY 10029, USA.
authors.forename: Eva Scheuring
authors.initials: ES
authors.lastname: Vanamee
authors.forename: Hector
authors.initials: H
authors.lastname: Viadiu
authors.forename: Siu-Hong
authors.initials: SH
authors.lastname: Chan
authors.forename: Ajay
authors.initials: A
authors.lastname: Ummat
authors.forename: Adrian M
authors.initials: AM
authors.lastname: Hartline
authors.forename: Shuang-yong
authors.initials: SY
authors.lastname: Xu
authors.forename: Aneel K
authors.initials: AK
authors.lastname: Aggarwal
mesh_terms: D000595:Amino Acid Sequence; D020134:Catalytic Domain; D004247:DNA / Q000737:chemistry*; D015245:Deoxyribonuclease BamHI / Q000737:chemistry; D015252:Deoxyribonucleases, Type II Site-Specific / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity
chemical_list: D004247:DNA; D015245:Deoxyribonuclease BamHI; D015252:Deoxyribonucleases, Type II Site-Specific