The PHA Depolymerase Engineering Database: A systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases
Polyhydroxyalkanoates (PHAs) can be degraded by many microorganisms using intra- or extracellular PHA depolymerases. PHA depolymerases are very diverse in sequence and substrate specificity, but share a common alpha/beta-hydrolase fold and a catalytic triad, which is also found in other alpha/beta hydrolases.
Results: The PHA Depolymerase Engineering Database (DED, http://www.ded.uni-stuttgart.de) has been established as a tool for systematic analysis of this enzyme family. The DED contains sequence entries of 587 PHA depolymerases, which were assigned to 8 superfamilies and 38 homologous families based on their sequence similarity.
For each family, multiple sequence alignments and profile hidden Markov models are provided, and functionally relevant residues are annotated.
Conclusion: The DED is a valuable tool which can be applied to identify new PHA depolymerase sequences from complete genomes in silico, to classify PHA depolymerases, to predict their biochemical properties, and to design enzyme variants with improved properties.
Author: Michael Knoll, Thomas M. Hamm, Florian Wagner, Virginia Martinez and Jurgen Pleiss
Credits/Source: BMC Bioinformatics 2009, 10:89
Published on: 2009-03-18
Copyright by the authors listed above - made available via BioMedCentral (Open Access). Please
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