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Title: The Lipase Engineering Database | P34 |
Fischer, Markus; Henke, Erik; Schmid, Rolf D; Pleiss, Jürgen Markus.Fischer@po.uni-stuttgart.de Institute of technical Biochemistry, University of Stuttgart |
| In the post-genomics era the understanding of sequence-structure-function relationships is of growing importance for predicting the biological function of gene products. Enormous amounts on sequence data have been generated by genome projects. Bioinformatics provides methods for organizing and analyzing these data efficiently and thus can help to reveal new insights into the biological role of enzymes. Here, we investigated the enzyme class of lipases (E.C. 3.1.1.3), which are widely used enzymes of which various biological data are available. To gain new biological knowledge on the sequence-structure-function relationship we developed the Lipase Engineering Database (LED) which integrates sequence, structure and mutant data. While the first version of the LED was set up on flat files (http://www.led.uni-stuttgart.de), the latest version is based on a relational database management system. For the underlying data model we developed an ontology, representing the sequence-structure-function relationships within the scope of lipases, but designed to be extensible and applicable also to other enzyme classes. This ontology based approach allowed us to improve our data mining tools and to develop a new set of data processing tools for representing, validating and integrating the extracted data. Thus, we have set up an environment, which is designed to easily create new enzyme databases and allows to efficiently gain new insights into the sequence-structure-function relationship of enzymes. Our concept of data integration has already proofed to be useful for protein engineering. By systematically investigating the fatty acid binding site of lipases a model was developed to understand experimentally observed mutant effects [1]. We also compared sequence and structure data to study the role of the functionally relevant oxyanion hole of lipases and classify two different types of signatures, which differ in sequence and structure [2]. It could be shown recently that this classification has important consequences for activity towards esters of tertiary alcohols [3]. |
| [1] J. Pleiss, M. Fischer, R. D. Schmid, Chem. Phys. Lipids 93 (1998) 67. [2] J. Pleiss, M. Fischer, M. Peiker, C. Thiele, R. D. Schmid, J. Mol. Catal. B: Enzymatic 10 (2000) 491. [3] E. Henke, J. Pleiss, U.T. Bornscheuer, Angew. Chem. ( in press ). |