Newman M, Strzelecka T, Dorner L F, Schildkraut I, Aggarwal A K
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032.
Structure. 1994 May 15;2(5):439-52. doi: 10.1016/s0969-2126(00)00045-9.
Type II restriction endonucleases recognize DNA sequences that vary between four to eight base pairs, and require only Mg2+ as a cofactor to catalyze the hydrolysis of DNA. Their protein sequences display a surprising lack of similarity, and no recurring structural motif analogous to the helix-turn-helix or the zinc finger of transcription factors, has yet been discovered.
We have determined the crystal structure of restriction endonuclease BamHI at 1.95 A resolution. The structure was solved by combining phase information derived from multi-wavelength X-ray data by algebraic and maximum likelihood methods. The BamHI subunit consists of a central beta-sheet with alpha-helices on both sides. The dimer configuration reveals a large cleft which could accommodate B-form DNA. Mutants of the enzyme that are deficient in cleavage are located at or near the putative DNA-binding cleft. BamHI and endonuclease EcoRI share a common core motif (CCM) consisting of five beta-strands and two helices. It remains to be determined if other restriction enzymes also contain the CCM.
The structure of BamHI provides the first clear evidence that there may be substantial structural homology amongst restriction enzymes, even though it is undetectable at the sequence level.
II型限制性内切核酸酶识别长度在4至8个碱基对之间变化的DNA序列，并且仅需要Mg2+作为辅助因子来催化DNA的水解。它们的蛋白质序列显示出惊人的缺乏相似性，并且尚未发现类似于转录因子的螺旋-转角-螺旋或锌指的重复结构基序。
我们已确定限制性内切核酸酶BamHI的晶体结构，分辨率为1.95埃。通过代数和最大似然法结合从多波长X射线数据获得的相位信息来解析该结构。BamHI亚基由一个中央β折叠组成，两侧为α螺旋。二聚体结构显示出一个大裂缝，可容纳B型DNA。在假定的DNA结合裂缝处或附近发现了切割缺陷的酶突变体。BamHI和内切核酸酶EcoRI共享一个由五条β链和两条螺旋组成的共同核心基序（CCM）。其他限制性酶是否也包含CCM还有待确定。
BamHI的结构提供了第一个明确的证据，表明限制性酶之间可能存在实质性的结构同源性，尽管在序列水平上无法检测到。
