The PHA Depolymerase Engineering Database: A systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases
<p>Abstract</p> <p>Background</p> <p>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...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2009-03-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/10/89 |
| _version_ | 1818565684873920512 |
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| author | Martinez Virginia Wagner Florian Hamm Thomas M Knoll Michael Pleiss Jürgen |
| author_facet | Martinez Virginia Wagner Florian Hamm Thomas M Knoll Michael Pleiss Jürgen |
| author_sort | Martinez Virginia |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>The PHA Depolymerase Engineering Database (DED, <url>http://www.ded.uni-stuttgart.de</url>) 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.</p> <p>Conclusion</p> <p>The DED is a valuable tool which can be applied to identify new PHA depolymerase sequences from complete genomes <it>in silico</it>, to classify PHA depolymerases, to predict their biochemical properties, and to design enzyme variants with improved properties.</p> |
| first_indexed | 2024-12-14T01:44:18Z |
| format | Article |
| id | doaj.art-e245c5aeb33643239341d70ca318b5ea |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-14T01:44:18Z |
| publishDate | 2009-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-e245c5aeb33643239341d70ca318b5ea2022-12-21T23:21:38ZengBMCBMC Bioinformatics1471-21052009-03-011018910.1186/1471-2105-10-89The PHA Depolymerase Engineering Database: A systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerasesMartinez VirginiaWagner FlorianHamm Thomas MKnoll MichaelPleiss Jürgen<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>The PHA Depolymerase Engineering Database (DED, <url>http://www.ded.uni-stuttgart.de</url>) 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.</p> <p>Conclusion</p> <p>The DED is a valuable tool which can be applied to identify new PHA depolymerase sequences from complete genomes <it>in silico</it>, to classify PHA depolymerases, to predict their biochemical properties, and to design enzyme variants with improved properties.</p>http://www.biomedcentral.com/1471-2105/10/89 |
| spellingShingle | Martinez Virginia Wagner Florian Hamm Thomas M Knoll Michael Pleiss Jürgen The PHA Depolymerase Engineering Database: A systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases BMC Bioinformatics |
| title | The PHA Depolymerase Engineering Database: A systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases |
| title_full | The PHA Depolymerase Engineering Database: A systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases |
| title_fullStr | The PHA Depolymerase Engineering Database: A systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases |
| title_full_unstemmed | The PHA Depolymerase Engineering Database: A systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases |
| title_short | The PHA Depolymerase Engineering Database: A systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases |
| title_sort | pha depolymerase engineering database a systematic analysis tool for the diverse family of polyhydroxyalkanoate pha depolymerases |
| url | http://www.biomedcentral.com/1471-2105/10/89 |
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