Abstract
BackgroundThe Lipase Engineering Database (LED) integrates information on sequence, structure and function of lipases, esterases and related proteins with the α/β hydrolase fold. A new superfamily for Candida antarctica lipase A (CALA) was introduced including the recently published crystal structure of CALA. Since CALA has a highly divergent sequence in comparison to other α/β hydrolases, the Lipase Engineering Database was used to classify CALA in the frame of the already established classification system. This involved the comparison of CALA to similar structures as well as sequence-based comparisons against the content of the LED.ResultsThe new release 3.0 (December 2009) of the Lipase Engineering Database contains 24783 sequence entries for 18585 proteins as well as 656 experimentally determined protein structures, including the structure of CALA. In comparison to the previous release [1] with 4322 protein and 167 structure entries this update represents a significant increase in data volume. By comparing CALA to representative structures from all superfamilies, a structure from the deacetylase superfamily was found to be most similar to the structure of CALA. While the α/β hydrolase fold is conserved in both proteins, the major difference is found in the cap region. Sequence alignments between both proteins show a sequence similarity of only 15%. A multisequence alignment of both protein families was used to create hidden Markov models for the cap region of CALA and showed that the cap region of CALA is unique among all other proteins of the α/β hydrolase fold. By specifically comparing the substrate binding pocket of CALA to other binding pockets of α/β hydrolases, the binding pocket of Candida rugosa lipase was identified as being highly similar. This similarity also applied to the lid of Candida rugosa lipase in comparison to the potential lid of CALA.ConclusionThe LED serves as a valuable tool for the systematic analysis of single proteins or protein families. The updated release 3.0 was used for the evaluation of α/β hydrolases. The HTML version of the database with new features is available at http://www.led.uni-stuttgart.de and provides sequences, structures and a set of analysis tools including phylogenetic trees and HMM profiles
Highlights
The Lipase Engineering Database (LED) integrates information on sequence, structure and function of lipases, esterases and related proteins with the a/b hydrolase fold
The LED is accessible by a web interface at http://www.led.uni-stuttgart. de
Most of the sequences of the superfamily abH38 have already been assigned to a common protein family in other protein family databases
Summary
The Lipase Engineering Database (LED) integrates information on sequence, structure and function of lipases, esterases and related proteins with the a/b hydrolase fold. Since CALA has a highly divergent sequence in comparison to other a/b hydrolases, the Lipase Engineering Database was used to classify CALA in the frame of the already established classification system This involved the comparison of CALA to similar structures as well as sequence-based comparisons against the content of the LED. Lipases (triacylglycerol hydrolases E.C. 3.1.1.3) are a versatile group of enzymes which catalyze the hydrolysis or synthesis of a broad range of water insoluble esters They belong to the class of a/b-hydrolases which contains esterases, acetylcholinesterases, cutinases, carboxylesterases and epoxide hydrolases. After its structure was recently determined [10], a detailed analysis of its structure identified CALA unambiguously as a member of the a/b hydrolase family In this structure the active site is not accessible to a substrate, the molecular details of substrate binding or the existence of a possible lid are still elusive
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