ArticleBMC genomics2010
Structural classification by the Lipase Engineering Database: a case study of Candida antarctica lipase A.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
20 citing papers in PubMed.
- Unraveling the regioselectivity of Ophiostoma piceae sterol esterase as a case study for lipases with wide acyl-binding tunnel entrances.The Journal of biological chemistry · 2026Article
- Tuning Selectivity in CalA Lipase: Beyond Tunnel Engineering.Biochemistry · 2023Article
- Novel CaLB-like Lipase Found Using ProspectBIO, a Software for Genome-Based Bioprospection.Biotech (Basel (Switzerland)) · 2023Article
- Investigation of Structural Features of Two Related Lipases and the Impact on Fatty Acid Specificity in Vegetable Fats.International journal of molecular sciences · 2022Article
- Production of 4-Ethyl Malate through Position-Specific Hydrolysis ofJournal of microbiology and biotechnology · 2022Article
- A flexible kinetic assay efficiently sorts prospective biocatalysts for PET plastic subunit hydrolysis.RSC advances · 2022Article
- Ethanol as additive enhance the performance of immobilized lipase LipA fromBiotechnology reports (Amsterdam, Netherlands) · 2021Article
- Increased mRNA Stability and Expression Level ofJournal of microbiology and biotechnology · 2021Article
- Metagenomic and Metatranscriptomic Analyses Revealed Uncultured Bacteroidales Populations as the Dominant Proteolytic Amino Acid Degraders in Anaerobic Digesters.Frontiers in microbiology · 2020Article
- Indoxyl Acetate as a Substrate for Analysis of Lipase Activity.International journal of analytical chemistry · 2019Article
- Molecular, biochemical and kinetic analysis of a novel, thermostable lipase (LipSm) fromJournal of biological research (Thessalonike, Greece) · 2018Article
- Alteration of Chain Length Selectivity ofAdvanced synthesis & catalysis · 2018Article
- Article
- Characterization of ML-005, a Novel Metaproteomics-Derived Esterase.Frontiers in microbiology · 2018Article
- Carboxylic ester hydrolases: Classification and database derived from their primary, secondary, and tertiary structures.Protein science : a publication of the Protein Society · 2016Review
- The genome of newly classified Ochroconis mirabilis: Insights into fungal adaptation to different living conditions.BMC genomics · 2016Article
- A combined bioinformatics and functional metagenomics approach to discovering lipolytic biocatalysts.Frontiers in microbiology · 2015Article
- Rhodococcus sp. strain CR-53 LipR, the first member of a new bacterial lipase family (family X) displaying an unusual Y-type oxyanion hole, similar to the Candida antarctica lipase clan.Applied and environmental microbiology · 2012Article
- Combinatorial reshaping of the Candida antarctica lipase A substrate pocket for enantioselectivity using an extremely condensed library.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Computer-Aided Protein Directed Evolution: a Review of Web Servers, Databases and other Computational Tools for Protein Engineering.Computational and structural biotechnology journal · 2012Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe Lipase Engineering Database (LED) integrates information on sequence, structure and function of lipases, esterases and related proteins with the alpha/beta 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 alpha/beta 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 alpha/beta 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 alpha/beta hydrolase fold. By specifically comparing the substrate binding pocket of CALA to other binding pockets of alpha/beta 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 alpha/beta 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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.