CYPSI: a structure-based interface for cytochrome P450s and ligands in Arabidopsis thaliana.
CYPSI: a structure-based interface for cytochrome P450s and ligands in Arabidopsis thaliana.
复制标题
CYPSI：拟南芥细胞色素 P450 和配体的基于结构的接口
DOI：
10.1186/1471-2105-13-332
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发表时间：
2012-12-20
影响因子：
3
通讯作者：
Su Z
中科院分区：
文献类型：
--
作者：
Zhang G;Zhang Y;Su Z
背景
细胞色素P450（CYP 450）超家族使陆生植物能够适应恶劣的环境。CYP是参与多种代谢途径的关键酶。在研究CYP与其底物之间的相互作用时，能够分析三维（3D）结构特别有用。然而，只有两个工厂的结构已经解决。此外，目前没有可用的数据库包含植物CYP和配体的结构信息。幸运的是，CYP的3D结构是高度保守的，这使得从基于模板的建模（TBM）中获得结构信息成为可能。
描述
网络结构界面（CYPSI）是一个网络结构研究的平台。CYPSI集成了266 A的3D结构。thaliana CYP预测的三个TBM方法：BMCD，我们专门开发的EST-TBM;和两个著名的网络服务器，MUSTER和I-TASSER。通过对模板的筛选和优化，BMCD构建的模型具有足够的准确性，可以用于实际应用，并通过一个寻找阿坝8′-羟基化CYP的对接实例进行了验证。CYPSI还为A. thaliana的结构和功能研究，包括400 PDB条目的解决CYP，48代谢途径与A。thaliana CYP，232个已报道的CYP配体和18个A.与配体对接的拟南芥CYP（总共61个复合物）。此外，CYPSI还包括搜索相似序列和化学物质的能力。
结论
CYPSI为A. thaliana CYP，这将有助于CYP和它们的底物之间的相互作用的调查。CYPSI有一个用户友好的界面，可以在http：//www.example.com上找到。bioinfo.cau.edu.cn/CYPSI
Background
The cytochrome P450 (CYP) superfamily enables terrestrial plants to adapt to harsh environments. CYPs are key enzymes involved in a wide range of metabolic pathways. It is particularly useful to be able to analyse the three-dimensional (3D) structure when investigating the interactions between CYPs and their substrates. However, only two plant CYP structures have been resolved. In addition, no currently available databases contain structural information on plant CYPs and ligands. Fortunately, the 3D structure of CYPs is highly conserved and this has made it possible to obtain structural information from template-based modelling (TBM).
Description
The CYP Structure Interface (CYPSI) is a platform for CYP studies. CYPSI integrated the 3D structures for 266 A. thaliana CYPs predicted by three TBM methods: BMCD, which we developed specifically for CYP TBM; and two well-known web-servers, MUSTER and I-TASSER. After careful template selection and optimization, the models built by BMCD were accurate enough for practical application, which we demonstrated using a docking example aimed at searching for the CYPs responsible for ABA 8′-hydroxylation. CYPSI also provides extensive resources for A. thaliana CYP structure and function studies, including 400 PDB entries for solved CYPs, 48 metabolic pathways associated with A. thaliana CYPs, 232 reported CYP ligands and 18 A. thaliana CYPs docked with ligands (61 complexes in total). In addition, CYPSI also includes the ability to search for similar sequences and chemicals.
Conclusions
CYPSI provides comprehensive structure and function information for A. thaliana CYPs, which should facilitate investigations into the interactions between CYPs and their substrates. CYPSI has a user-friendly interface, which is available athttp://bioinfo.cau.edu.cn/CYPSI.
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