Structural characterisation of alpha/beta-hydrolases

An update of the Lipase Engineering Database: systematic analysis of sequences and structures of a large protein family.

The Lipase Engeneering Database (LED) integrates information on sequence, structure and function of alpha/beta-hydrolases. This protein class is comprised of enzymes with various functions that share structural rather than sequence similarities. As part of updating the LED we analysed the structures of the proteins in the current version of the LED.

This analysis showed that alpha/beta-hydrolases all share the same core fold but can be distinguished by additional modules. These allow a classification into different architectures and hence we are developing a new structure-based classification of alpha/beta-hydrolases.

For these different architectures, features like the accessibility of the active centre are investigated. Furthermore collective movements of residues within alpha/beta-hydrolases are analysed by essential dynamics simulation to determine the movement of the identified modules. The overall goal is to set up a new architecture-based version of the Lipase Engineering Database and to characterise alpha/beta-hydrolases of each architecture type.

Publications

  1. Widmann, M., Juhl, P., & Pleiss, J. (2010). Structural classification by the Lipase Engineering Database: a case study of Candida antarctica lipase A. BMC Genomics, 11, 123.
  2. Fischer, M., & Pleiss, J. (2003). The Lipase Engineering Database: a navigation and analysis tool for protein families. Nucleic Acids Res, 31, 319–321.
  3. Pleiss, J., Fischer, M., Peiker, M., Thiele, C., & Schmid, R. (2000). Lipase Engineering Database: understanding and exploiting sequence-structure-function relationships. J Mol Catal B: Enzym, 10, 491–508.
  4. Pleiss, J., Fischer, M., & Schmid, R. (1998). Anatomy of lipase binding sites: the scissile fatty acid binding site. Chem Phys Lipids, 93, 67–80.

Project Members

Tabea Bauer
 

Tabea Bauer

Bioinformatics

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