Asymmetric DNA recognition by the OkrAI endonuclease, an isoschizomer of BamHI.
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.
Vanamee
Eva Scheuring
ES
Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, NY 10029, USA.
Viadiu
Hector
H
Chan
Siu-Hong
SH
Ummat
Ajay
A
Hartline
Adrian M
AM
Xu
Shuang-yong
SY
Aggarwal
Aneel K
AK
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
D004247:DNA; D015245:Deoxyribonuclease BamHI; D015252:Deoxyribonucleases, Type II Site-Specific