Sirim Demet, Widmann Michael, Wagner Florian, Pleiss Jürgen
Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
BMC Struct Biol. 2010 Oct 15;10:34. doi: 10.1186/1472-6807-10-34.
Cytochrome P450 monooxygenases (CYPs) form a vast and diverse family of highly variable sequences. They catalyze a wide variety of oxidative reactions and are therefore of great relevance in drug development and biotechnological applications. Despite their differences in sequence and substrate specificity, the structures of CYPs are highly similar. Although being in research focus for years, factors mediating selectivity and activity remain vague.
This systematic comparison of CYPs based on the Cytochrome P450 Engineering Database (CYPED) involved sequence and structure analysis of more than 8000 sequences. 31 structures have been applied to generate a reliable structure-based HMM profile in order to predict structurally conserved regions. Therefore, it was possible to automatically transfer these modules on CYP sequences without any secondary structure information, to analyze substrate interacting residues and to compare interaction sites with redox partners.
Functionally relevant structural sites of CYPs were predicted. Regions involved in substrate binding were analyzed in all sequences among the CYPED. For all CYPs that require a reductase, two reductase interaction sites were identified and classified according to their length. The newly gained insights promise an improvement of engineered enzyme properties for potential biotechnological application. The annotated sequences are accessible on the current version of the CYPED. The prediction tool can be applied to any CYP sequence via the web interface at http://www.cyped.uni-stuttgart.de/cgi-bin/strpred/dosecpred.pl.
细胞色素P450单加氧酶（CYPs）构成了一个庞大且多样的家族，其序列高度可变。它们催化各种各样的氧化反应，因此在药物开发和生物技术应用中具有重要意义。尽管它们在序列和底物特异性上存在差异，但CYPs的结构高度相似。尽管多年来一直是研究重点，但介导选择性和活性的因素仍不明确。
基于细胞色素P450工程数据库（CYPED）对CYPs进行的这种系统比较涉及对8000多个序列的序列和结构分析。已应用31种结构来生成可靠的基于结构的隐马尔可夫模型（HMM）概况，以预测结构保守区域。因此，有可能在没有任何二级结构信息的情况下，将这些模块自动转移到CYP序列上，分析底物相互作用残基，并将相互作用位点与氧化还原伙伴进行比较。
预测了CYPs功能相关的结构位点。在CYPED中的所有序列中分析了参与底物结合的区域。对于所有需要还原酶的CYPs，确定了两个还原酶相互作用位点，并根据其长度进行了分类。新获得的见解有望改善工程酶的特性，以用于潜在的生物技术应用。注释序列可在CYPED的当前版本中获取。预测工具可通过网页界面http://www.cyped.uni-stuttgart.de/cgi-bin/strpred/dosecpred.pl应用于任何CYP序列。
