Crystal structure of an IclR homologue from Microbacterium sp. strain HM58-2
Crystal structure of an IclR homologue from Microbacterium sp. strain HM58-2
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微杆菌属 IclR 同源物的晶体结构。
DOI：
10.1107/s2053230x16019208
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发表时间：
2017
期刊：
影响因子：
--
通讯作者：
Shunsuke Yajima
中科院分区：
文献类型：
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作者：
Tomonori Akiyama;Yusuke Yamada;Naoki Takaya;Shinsaku Ito;Yasuyuki Sasaki;Shunsuke Yajima
细菌转录因子IclR（isocitrate lyase regulator，异柠檬酸裂解酶调节子）是单组分信号转导系统的成员，其共享连接至底物结合结构域（substrate binding domain，SBD）的螺旋-转角-螺旋（helix-turn-helix，HTH）型DNA结合结构域（DBD）的共同基序。在这里，报道了来自微杆菌属菌株HM 58 -2的IclR同源物（Mi-IclR）的晶体结构，其分解代谢酰肼作为唯一碳源。预期Mi-IclR调节负责酰肼降解的操纵子作为初始步骤。本机单波长异常衍射（SAD）的实验进行了分子置换相结合。来自CCP 4套件的CRANK 2成功地定相和建模了由不对称单元中的1000个残基组成的同源四聚体的完整结构，并且该模型被细化到2.1 μ m分辨率。 Mi-IclR的整体结构与其他已知的IclR结构共享相同的结构域组合，但DBD和SBD之间的相对几何形状不同。因此，Mi-IclR四聚体的几何形状是独特的：每个亚基中的推定的底物结合位点可以从四聚体的外部接近，而不是像先前已知的IclR结构那样埋在内部。结构域几何结构的这些差异可能有助于IclRs的转录调控。
The bacterial transcription factor IclR (isocitrate lyase regulator) is a member of a one-component signal transduction system, which shares the common motif of a helix–turn–helix (HTH)-type DNA-binding domain (DBD) connected to a substrate-binding domain (SBD). Here, the crystal structure of an IclR homologue (Mi-IclR) from Microbacterium sp. strain HM58-2, which catabolizes acylhydrazide as the sole carbon source, is reported. Mi-IclR is expected to regulate an operon responsible for acylhydrazide degradation as an initial step. Native single-wavelength anomalous diffraction (SAD) experiments were performed in combination with molecular replacement. CRANK2 from the CCP4 suite successfully phased and modelled the complete structure of a homotetramer composed of 1000 residues in an asymmetric unit, and the model was refined to 2.1 Å resolution. The overall structure of Mi-IclR shared the same domain combination as other known IclR structures, but the relative geometry between the DBD and SBD differs. Accordingly, the geometry of the Mi-IclR tetramer was unique: the putative substrate-binding site in each subunit is accessible from the outside of the tetramer, as opposed to buried inside as in the previously known IclR structures. These differences in the domain geometry may contribute to the transcriptional regulation of IclRs.