Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications
Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications
复制标题
DOI：
10.1073/pnas.0409851102
复制
发表时间：
2005-03-01
影响因子：
11.1
通讯作者：
Kim, SH
中科院分区：
文献类型：
--
作者：
Kim, JS;DeGiovanni, A;Kim, SH
I型限制性修饰酶与II型和III型酶的区别在于，它们能够识别由给定间隔段分隔的两个特定的dsDNA序列，并将DNA随机地从识别位点切割开。它们是由三个亚基组成的寡聚蛋白：特异性亚基、甲基化亚基和限制性亚基。我们在2.4埃的分辨率下解决了jannaschii甲烷球菌特异性亚基的晶体结构。两个高度保守区（CRs）在中间和在C端形成一个长反平行的螺旋线圈。两个目标识别域形成球状结构，具有几乎相同的拓扑结构和两个独立的DNA结合裂缝，模型DNA螺旋轴位于CR螺旋上。这一结构表明，螺旋状CRs作为一个分子标尺，用于区分两个已识别的DNA序列。此外，两个DNA结合裂缝的相对方向表明，结合的dsDNA发生了扭结，目标腺嘌呤从已识别的DNA序列中暴露出来。
Type I restriction-modification enzymes are differentiated from type II and type III enzymes by their recognition of two specific dsDNA sequences separated by a given spacer and cleaving DNA randomly away from the recognition sites. They are oligomeric proteins formed by three subunits: a specificity subunit, a methylation subunit, and a restriction subunit. We solved the crystal structure of a specificity subunit from Methanococcus jannaschii at 2.4-Angstrom resolution. Two highly conserved regions (CRs) in the middle and at the C terminus form a coiled-coil of long antiparallel alpha-helices. Two target recognition domains form globular structures with almost identical topologies and two separate DNA binding clefts with a modeled DNA helix axis positioned across the CR helices. The structure suggests that the coiled-coil CRs act as a molecular ruler for the separation between two recognized DNA sequences. Furthermore, the relative orientation of the two DNA binding clefts suggests kinking of bound dsDNA and exposing of target adenines from the recognized DNA sequences.