Konarev Petr V, Kachalova Galina S, Ryazanova Alexandra Yu, Kubareva Elena A, Karyagina Anna S, Bartunik Hans D, Svergun Dmitri I
European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany.
Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russia.
PLoS One. 2014 Apr 7;9(4):e93453. doi: 10.1371/journal.pone.0093453. eCollection 2014.
(Cytosine-5)-DNA methyltransferase SsoII (M.SsoII) consists of a methyltransferase domain (residues 72-379) and an N-terminal region (residues 1-71) which regulates transcription in SsoII restriction-modification system. Small-angle X-ray scattering (SAXS) is employed here to study the low resolution structure of M.SsoII and its complex with DNA containing the methylation site. The shapes reconstructed ab initio from the SAXS data reveal two distinct protein domains of unequal size. The larger domain matches the crystallographic structure of a homologous DNA methyltransferase HhaI (M.HhaI), and the cleft in this domain is occupied by DNA in the model of the complex reconstructed from the SAXS data. This larger domain can thus be identified as the methyltransferase domain whereas the other domain represents the N-terminal region. Homology modeling of the M.SsoII structure is performed by using the model of M.HhaI for the methyltransferase domain and representing the N-terminal region either as a flexible chain of dummy residues or as a rigid structure of a homologous protein (phage 434 repressor) connected to the methyltransferase domain by a short flexible linker. Both models are compatible with the SAXS data and demonstrate high mobility of the N-terminal region. The linker flexibility might play an important role in the function of M.SsoII as a transcription factor.
（胞嘧啶-5）-DNA甲基转移酶SsoII（M.SsoII）由一个甲基转移酶结构域（第72至379位氨基酸残基）和一个N端区域（第1至71位氨基酸残基）组成，该N端区域在SsoII限制修饰系统中调节转录。本文采用小角X射线散射（SAXS）研究M.SsoII及其与含甲基化位点的DNA复合物的低分辨率结构。从SAXS数据从头重建的形状揭示了两个大小不等的不同蛋白质结构域。较大的结构域与同源DNA甲基转移酶HhaI（M.HhaI）的晶体结构匹配，在从SAXS数据重建的复合物模型中，该结构域的裂隙被DNA占据。因此，这个较大的结构域可被鉴定为甲基转移酶结构域，而另一个结构域代表N端区域。通过使用M.HhaI的模型构建甲基转移酶结构域，并将N端区域表示为虚拟残基的柔性链或通过短柔性接头连接到甲基转移酶结构域的同源蛋白（噬菌体434阻遏物）的刚性结构，对M.SsoII结构进行同源建模。这两个模型均与SAXS数据兼容，并显示出N端区域的高流动性。接头的柔性可能在M.SsoII作为转录因子的功能中起重要作用。
