Summary information and primary citation
- PDB-id
- 3odh; SNAP-derived features in text and JSON formats;
DNAproDB
- Class
- hydrolase-DNA
- Method
- X-ray (2.3 Å)
- Summary
- Structure of okrai-DNA complex
- Reference
- Vanamee ES, Viadiu H, Chan SH, Ummat A, Hartline AM, Xu SY, Aggarwal AK (2011): "Asymmetric DNA recognition by the OkrAI endonuclease, an isoschizomer of BamHI." Nucleic Acids Res., 39, 712-719. doi: 10.1093/nar/gkq779.
- 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.
