The Lipase Engineering Database (LED) version4.1.0
part of the BioCatNet
This Internet database integrates information on sequence, structure and function of lipases and related proteins sharing the same a/b hydrolase fold.
The BioCatNet Database System aims to collect and present comprehensive information about biocatalysts: sequence, structure, educts, products, environmental conditions and kinetics. Moreover, it will reveal structure-function relationships to boost development of novel biocatalysts.
To contribute to BioCatNet by submission of functional information, please refer to the information in the BioCatNet Wiki.
The LED was build based on the different architectures of α/β‐hydrolases. All α/β‐hydrolases consist of a catalytically active core domain (the α/β‐hydrolase fold), containing the catalytic triad and the oxyanion hole. They might also contain additional structural modules, such as a lid, a cap, and N‐ or C‐terminal domains. The lid can emerge from five different positions: between β‐strands β+1/β+2, β‐1/β0, β‐4/β‐3, β+3/β+4, or between the N‐terminus and β‐3. Further, they can contain single caps, double caps, or N‐terminal caps, and a N-terminal or a C-terminal domain. The presence of these structural modules determine the architecture of the α/β‐hydrolase, resulting in 12 superfamilies. In addition, α/β‐hydrolases can be distinguished by their oxyanion hole signature (GX‐, GGGX‐, or Y‐type), which is indicated for each homologous family. For all homologous families with available structure information, the catalytic triad, the oxyanion hole residues, and the structural modules are annotated.
The LED release 3.0 (2009) is still accessible at www.led.uni-stuttgart.de.
Bauer T., Buchholz P. C. F. & Pleiss J. (2019). The modular structure of α/β-hydrolases.The FEBS Journal 287(5): 1035-1053
Widmann M., Trodler P. & Pleiss J. (2010). The isoelectric region of proteins: a systematic analysis. PLoS One 5: e10546
Widmann M., Juhl PB. & Pleiss J. (2010). Structural classification by the Lipase Engineering Database: a case study of Candida antarctica lipase A. BMC Genomics 11: 123
Widmann M., Clairo M., Dippon J. & Pleiss J. (2008). Analysis of the distribution of functionally relevant rare codons. BMC Genomics 9: 207
Koschorreck M., Fischer M., Barth S. & Pleiss J. (2005). How to find soluble proteins: a comprehensive analysis of alpha/beta hydrolases for recombinant expression in E. coli. BMC Genomics 6: 49
Barth S., Fischer M., Schmid R.D. & Pleiss J. (2004). The database of epoxide hydrolases and haloalkane dehalogenases: one structure, many functions. Bioinformatics 20: 2845-2847
Barth S., Fischer M., Schmid R.D. & Pleiss J. (2004). Sequence and structure of epoxide hydrolases: a systematic analysis. Proteins 55: 846-855
Fischer M. & Pleiss J. (2003). The Lipase Engineering Database: a navigation and analysis tool for protein families. Nucleic Acids Res 31: 319-321
Pleiss J., Fischer M., Peiker M., Thiele C. & Schmid R.D. (2000). Lipase Engineering Database: understanding and exploiting sequence-structure-function relationships. J Mol Catal B: Enzymatic 10: 491 -508
Pleiss J., Scheib H., Schmid R.D. (2000). The his gap motif in microbial lipases: a determinant of stereoselectivity toward triacylglycerols and analogs. Biochimie 82: 1043-1052
Pleiss J., Fischer M., Schmid R.D. (1998). Anatomy of lipase binding sites: the scissile fatty acid binding site. Chem Phys Lipids 93: 67-80