Institute of Technical Biochemistry, University of Stuttgart, Germany.
BMC Biochem. 2009 Nov 12;10:27. doi: 10.1186/1471-2091-10-27.
Cytochrome P450 monooxygenases (CYPs) form a vast and diverse enzyme class of particular interest in drug development and a high biotechnological potential. Although very diverse in sequence, they share a common structural fold. For the comprehensive and systematic comparison of protein sequences and structures the Cytochrome P450 Engineering Database (CYPED) was established. It was built up based on an extensible data model that enables its functions readily enhanced.
The new version of the CYPED contains information on sequences and structures of 8613 and 47 proteins, respectively, which strictly follow Nelson's classification rules for homologous families and superfamilies. To gain biochemical information on substrates and inhibitors, the CYPED was linked to the Cytochrome P450 Knowledgebase (CPK). To overcome differences in the data model and inconsistencies in the content of CYPED and CPK, a metric was established based on sequence similarity to link protein sequences as primary keys. In addition, the annotation of structurally and functionally relevant residues was extended by a reliable prediction of conserved secondary structure elements and by information on the effect of single nucleotide polymorphisms.
The online accessible version of the CYPED at http://www.cyped.uni-stuttgart.de provides a valuable tool for the analysis of sequences, structures and their relationships to biochemical properties.
细胞色素 P450 单加氧酶（CYPs）形成了一个庞大而多样化的酶类，在药物开发中特别有趣，具有很高的生物技术潜力。尽管它们在序列上非常多样化，但它们具有共同的结构折叠。为了全面系统地比较蛋白质序列和结构，建立了细胞色素 P450 工程数据库（CYPED）。它是基于一个可扩展的数据模型构建的，能够轻松增强其功能。
新版本的 CYPED 包含了 8613 个序列和 47 个蛋白质结构的信息，这些序列和结构严格遵循 Nelson 对同源家族和超家族的分类规则。为了获得关于底物和抑制剂的生化信息，CYPED 与细胞色素 P450 知识库（CPK）进行了链接。为了克服 CYPED 和 CPK 数据模型的差异和内容的不一致性，建立了一个基于序列相似性的度量标准，将蛋白质序列作为主键进行链接。此外，通过可靠的保守二级结构元素预测和单核苷酸多态性影响的信息，扩展了结构和功能相关残基的注释。
可在线访问的 CYPED 版本位于 http://www.cyped.uni-stuttgart.de，为分析序列、结构及其与生化特性的关系提供了有价值的工具。
