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Updated: Jun 16, 2026
08:59
Defining Substrate Specificities for Lipase and Phospholipase Candidates
Published on: November 23, 2016
Structural classification by the Lipase Engineering Database: a case study of Candida antarctica lipase A
Michael Widmann1, P Benjamin Juhl, Jürgen Pleiss
1Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
BMC Genomics
|February 23, 2010
Summary
The Lipase Engineering Database (LED) now classifies Candida antarctica lipase A (CALA) within the alpha/beta hydrolase fold. CALA exhibits unique structural features, particularly in its cap region, despite sequence similarities to other lipases.
Area of Science:
- Biochemistry
- Structural Biology
- Bioinformatics
Background:
- The Lipase Engineering Database (LED) curates sequence, structure, and function data for lipases, esterases, and related alpha/beta hydrolase fold proteins.
- Candida antarctica lipase A (CALA) was recently classified into a new superfamily due to its highly divergent sequence compared to other alpha/beta hydrolases.
Purpose of the Study:
- To classify CALA within the established framework of the Lipase Engineering Database.
- To analyze the structural and sequence characteristics of CALA in relation to other alpha/beta hydrolases.
Main Methods:
- Utilized the Lipase Engineering Database for sequence and structure-based comparisons.
- Performed structural comparisons of CALA against representative superfamilies within the LED.
- Conducted sequence alignments and generated Hidden Markov Models (HMMs) for the cap region of CALA.
Main Results:
- Release 3.0 of the LED includes 24,783 sequence entries and 656 protein structures.
- CALA shares the highest structural similarity with proteins from the deacetylase superfamily, despite only 15% sequence similarity.
- CALA possesses a unique cap region among alpha/beta hydrolases, and its substrate binding pocket is highly similar to that of Candida rugosa lipase.
Conclusions:
- The LED is a valuable resource for systematic analysis of protein families like alpha/beta hydrolases.
- Release 3.0 provides an updated and expanded dataset for protein evaluation.
- The LED offers analysis tools, including phylogenetic trees and HMM profiles, accessible via its HTML interface.
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