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The PHA Depolymerase Engineering Database: A systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases

Michael Knoll1, Thomas M Hamm1, Florian Wagner1, Virginia Martinez2 and Jürgen Pleiss1*

Author Affiliations

1 Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany

2 Department of Molecular Microbiology, Centro de Investigaciones Biologicas Ramiro de Maeztu, 9, 28040 Madrid, Spain

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BMC Bioinformatics 2009, 10:89  doi:10.1186/1471-2105-10-89

Published: 18 March 2009

Abstract

Background

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 α/β-hydrolase fold and a catalytic triad, which is also found in other α/β-hydrolases.

Results

The PHA Depolymerase Engineering Database (DED, http://www.ded.uni-stuttgart.de webcite) 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.