Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, NY 10029, USA.
Nucleic Acids Res. 2011 Jan;39(2):712-9. doi: 10.1093/nar/gkq779. Epub 2010 Sep 9.
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.
限制酶除了同裂酶（即识别和切割相同 DNA 序列的酶）外，彼此之间序列同源性很小或没有。我们在此展示了与 BamHI 共结晶的相同 DNA 序列（TATGGATCCATA）结合的 BamHI 同裂酶 OkrAI 的结构。我们表明，OkrAI 是 BamHI 的更简化版本，不仅缺失 N 端和 C 端螺旋，而且还缺失内部 3(10)螺旋，并且包含的 β-折叠比 BamHI 中的更短。尽管存在这些结构差异，但 OkrAI 以与 BamHI 非常相似的方式识别 DNA，包括通过 C 端“臂”进行不对称接触，这些臂似乎通过“竞争”较小的沟道来发挥作用。然而，这些臂比 BamHI 中的更短。我们观察到 OkrAI 和 BamHI 之间具有相似的 DNA 结合亲和力，但与 BamHI 相比，OkrAI 的星活性（在 37°C 时）更高。总之，OkrAI 和 BamHI 的结构提供了一个难得的机会，可以比较两种作用于完全相同 DNA 底物的限制酶。
