The PHA Depolymerase Engineering Database: A systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases
© Knoll et al; licensee BioMed Central Ltd. 2009
Received: 28 November 2008
Accepted: 18 March 2009
Published: 18 March 2009
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.
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.
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.
In the past decade, polyhydroxyalkanoates (PHAs) gained industrial interest as biodegradable substitutes for non-degradable plastics. While poly (R)-3-hydroxybutyric acid (PHB) is the most widely studied and the best characterized PHA, a wide variety of PHAs with differences in flexibility and thermostability have been described. Many bacteria accumulate PHAs as storage compounds of carbon and energy [1–3]. PHAs have been assigned to two classes, depending on the number of carbon atoms of the monomers: short chain length PHAs (PHASCL) with 3 to 5 carbon atoms per monomer and medium chain length PHAs (PHAMCL) with 6 to 15 carbon atoms per monomer. PHAs are degraded by intracellular and extracellular PHA depolymerases. Intracellular PHA depolymerases hydrolyze an endogenous carbon reservoir, the native PHA granules, consisting of the polymer with a surface layer of proteins and phospholipids. Extracellular PHA depolymerases degrade denatured extracellular granules which are partially crystalline and are lacking a surface layer [4, 5]. Thus, depending on their substrate and its physical state, PHA depolymerases are grouped generally into four families: PHA depolymerases degrading the native intracellular granules (nPHAMCL depolymerases and nPHASCL depolymerases) and PHA depolymerases degrading the denatured extracellular PHA granules (dPHAMCL depolymerases and dPHASCL depolymerases). One exception of this classification is an extracellular nPHASCL depolymerase from Paucimonas lemoignei which is active only against native PHA granules . Additionally periplasmatic PHA depolymerases exist, as a PHA depolymerase from Rhodospirillum rubrum has been described recently to be located in the periplasm .
PHA depolymerases are carboxylesterases and belong to the α/β-hydrolase fold family .
As member of the α/β-hydrolase fold, two families including PHA depolymerases have also been described in the Pfam proteins families database : the family of Esterase PHB depolymerases (Pfam accession code: PF10503) and the family describing the C-terminus of bacterial PHB depolymerases (Pfam accession code: PF06850).
With exception of a few intracellular nPHASCL depolymerases, all PHA depolymerases have a catalytic triad (serine – histidine – aspartic acid) as active site. The catalytic serine is embedded in a GxSxG sequence motif (known as 'lipase box') as found in other α/β-hydrolases. Additionally, a conserved non-catalytic histidine near the oxyanion hole is found analogous to lipases [5, 9]. The best studied PHA depolymerases are dPHASCL depolymerases. They share a common domain architecture consisting of a short signal peptide, a catalytic domain (including the lipase box and the oxyanion hole), a short linker domain, and a substrate binding domain . Depending on the location of the lipase box on sequence level relative to the oxyanion hole, two types of catalytic domains are known. Within the sequences of type 1 catalytic domains, the oxyanion hole can be found N-terminal to the lipase box, similar to lipases. Within the sequences of type 2 catalytic domains, the oxyanion hole is found C-terminal to the catalytic triad. In contrast to dPHASCL depolymerases, dPHAMCL depolymerases possess no substrate binding domain. In these enzymes, the N-terminal region of the catalytic domain is assumed to function as substrate binding site .
The PHA depolymerase from Rhodospirillum rubrum which is described to be located in the periplasm  is a special case, as it has a catalytic domain similar to extracellular PHA depolymerases with a catalytic domain type 2.
For intracellular nPHA depolymerases no particular substrate binding domain has been described so far. A few intracellular nPHASCL depolymerases have no lipase box, but have a catalytic triad consisting of cysteine, histidine, and aspartic acid. One member of this family is the nPHASCL depolymerase of Ralstonia eutropha .
Only about 30 PHA depolymerases with experimentally validated PHA depolymerase activity have been described so far. The factors which mediate the capability of depolymerases to degrade PHAs with high specificity are not yet understood. Although the sequence similarity of PHA depolymerases to other known α/β-hydrolases like lipases and esterases is low and substrate specificity differs considerably, they belong to the same fold family and possess a highly conserved active site. From a systematic comparison of the PHA depolymerase family to other α/β-hydrolases, depolymerase-specific motifs can be derived. However, a data resource is still lacking which integrates sequence and structure information and provides tools for a systematic analysis of the sequence-structure-function relationship of PHA depolymerases. Therefore, the PHA Depolymerase Engineering Database (DED, http://www.ded.uni-stuttgart.de) has been designed to assist a comprehensive analysis of sequences, the annotation of new sequences and the design of mutants. For the analysis of lipases and esterases, the Lipase Engineering Database (LED, http://www.led.uni-stuttgart.de) has previously been established and applied [12, 13]. Comparison of the rules derived from the LED to the DED will help to understand differences of PHA depolymerases and other α/β-hydrolases, and will relate experimentally observed properties of PHA depolymerases to their sequence.
Construction and content
Experimentally validated PHA depolymerases, which were used as seed sequences to set up the DED.
Accession number (gi)
Ralstonia eutropha H16
Intracellular nPHASCL depolymerases (no lipase box)
Bacillus thuringiensis serovar israelensis ATCC 35646
Intracellular nPHASCL depolymerases (lipase box)
Periplasmatic PHA depolymerases
Intracellular nPHAMCL depolymerases
Extracellular dPHASCL depolymerises (catalytic domain type 1)
Acidovorax sp. TP4
Extracellular dPHASCL depolymerises (catalytic domain type 2)
Schlegelella sp. KB1a
Extracellular nPHASCL depolymerases
Extracellular dPHAMCL depolymerases
▪ intracellular nPHASCL depolymerases (no lipase box)
▪ intracellular nPHASCL depolymerases (lipase box)
▪ intracellular nPHAMCL depolymerases
▪ periplasmatic PHA depolymerases
▪ extracellular dPHASCL depolymerases (catalytic domain type 1)
▪ extracellular dPHASCL depolymerases (catalytic domain type 2)
▪ extracellular nPHASCL depolymerases
▪ extracellular dPHAMCL depolymerases
Sequence entries with more than 98% sequence identity, which originate from the same source organism, were assigned to a single protein entry. In case of multiple sequence entries for one protein, the longest sequence was set as reference sequence. For protein entries with available structure information, structural monomers were downloaded from the Protein Data Bank  and stored as structure entries. Secondary structure information was calculated applying the program DSSP  and displayed in the annotated multiple sequence alignments which are generated using ClustalW (v1.83) with default parameters . Annotation information on structurally or functionally relevant residues (active site, disulfide bridges, signal peptide) was extracted from the NCBI entries and annotated in the DED. Information on experimentally validated depolymerases was manually added. Residues of the lipase box and the catalytic triad were manually annotated, which enables an easy identification of these residues for almost all PHA depolymerases based on multiple sequence alignments.
The PHA Depolymerase Engineering Database consists of 735 sequence entries which code for 587 different proteins. The proteins have been assigned to 8 superfamilies and 38 homologous families. The largest PHA depolymerase families are the intracellular nPHASCL depolymerases (no lipase box) and the extracellular dPHASCL depolymerases (catalytic domain type 1) with 224 and 234 protein entries, respectively, and account for 38% and 39% of all protein entries. Only one member of the family of periplasmatic PHA depolymerases was found, the PHA depolymerase of Rhodospirillum rubrum. For the families of extracellular dPHASCL depolymerases (catalytic domain type 2) and the family of extracellular nPHASCL depolymerases, structure information is available. Interestingly, two proteins from Cupriavidus taiwanensis and Ralstonia eutropha H16 which are annotated as "intracellular PHA depolymerase" in the GenBank were assigned to the family of extracellular dPHASCL depolymerases (catalytic domain type 1) due to their sequence similarity (gi: 194292521, gi:74267419 ). The latter is reported to be highly active against artificial amorphous PHB granules, and is lacking a signal peptide, a linker domain, and a substrate binding domain. Another exception is the PHA depolymerase from Pseudomonas sp. which is annotated as "extracellular PHA depolymerase" in the GenBank but was assigned to the family of intracellular nPHAMCL depolymerases in the DED (gi:34452171).
Utility and discussion
The DWARF system is an integrative bioinformatics tool to build up protein family databases into a local data warehouse system. The DWARF system has previously been successfully applied to build up the Lipase Engineering Database [12, 13], the Cytochrome P450 Engineering Database http://www.cyped.uni-stuttgart.de, and the Medium-Chain Dehydrogenase/Reductase Engineering Database http://www.mdred.uni-stuttgart.de. A local data warehouse has the advantage of a common and consistent data structure which enables systematic analysis of complete protein families. The DED is the first data source that integrates information on sequence, structure, and function of PHA depolymerases in a systematic and consistent format.
The database can be browsed on the level of sequence, structure, or organism. All protein entries are linked to the respective NCBI entries. Annotated multiple sequence alignments and phylogenetic trees that are visualized applying the program PHYLODENDRON http://iubio.bio.indiana.edu/soft/molbio/java/apps are provided via the online accessible version of the DED at http://www.ded.uni-stuttgart.de. For each family, information of amino acid conservation is given as calculated by PLOTCON . For each homologous family and superfamily, family-specific profile hidden Markov models were calculated by the HMMER program http://hmmer.janelia.org/ to assist the classification of new PHA depolymerase sequences and the identification of new PHA depolymerase sequences from complete genomes in silico. A local BLAST interface is available to perform a BLAST search against the DED. A new dynamic user interface was developed which enables fast and easy integration of updated versions of the DED. The DED will be regularly updated by an automated script. For new sequence entries referring to a new structure in the Protein Data Bank (PDB), structure information is updated as well. New sequence and structure entries are classified into the homologous families and superfamilies based on their sequence identity.
The PHA Depolymerase Engineering Database (DED) has been designed to serve as a navigation and analysis tool of PHA depolymerases. It serves as a platform to analyze sequence-structure-function relationships and to classify new sequences by providing multiple sequence alignments, phylogenetic trees, and family-specific profiles. The DED hence provides a valuable source of information to investigate the family of PHA depolymerases in a systematic way, to identify new proteins from genomes, and to distinguish between PHA depolymerases and lipases. Thus, it paves the way for a deeper understanding of biochemical properties of PHA depolymerases and to design PHA depolymerases with improved properties.
Availability and requirements
The PHA Depolymerase Engineering Database (DED) is online accessible at http://www.ded.uni-stuttgart.de. All information on families of sequence and structure data, as well as alignments, phylogenetic trees, and family-specific profiles can be accessed by manual download.
M.A. Prieto and D. Jendrossek are gratefully acknowledged for fruitful discussions. The work was carried out in the framework of the IP-project 'Sustainable Microbial and Biocatalytic Production of Advanced Functional Materials' (BIOPRODUCTION/NMP-2-CT-2007-026515) funded by the European Commission.
- Anderson AJ, Dawes EA: Occurrence, metabolism, metabolic role, and industrial uses of bacterial polyhydroxyalkanoates. Microbiol Rev 1990, 54(4):450–472.PubMed CentralPubMedGoogle Scholar
- Prieto MA: From oil to bioplastics, a dream come true? Journal of Bacteriology 2007, 189(2):289–290. 10.1128/JB.01576-06PubMed CentralView ArticlePubMedGoogle Scholar
- Garcia B, Olivera ER, Minambres B, Fernandez-Valverde M, Canedo LM, Prieto MA, Garcia JL, Martinez M, Luengo JM: Novel biodegradable aromatic plastics from a bacterial source – Genetic and biochemical studies on a route of the phenylacetyl-CoA catabolon. Journal of Biological Chemistry 1999, 274(41):29228–29241. 10.1074/jbc.274.41.29228View ArticlePubMedGoogle Scholar
- Tokiwa Y, Calabia BP: Degradation of microbial polyesters. Biotechnol Lett 2004, 26(15):1181–1189. 10.1023/B:BILE.0000036599.15302.e5View ArticlePubMedGoogle Scholar
- Jendrossek D, Handrick R: Microbial degradation of polyhydroxyalkanoates. Annu Rev Microbiol 2002, 56: 403–432. 10.1146/annurev.micro.56.012302.160838View ArticlePubMedGoogle Scholar
- Handrick R, Reinhardt S, Focarete ML, Scandola M, Adamus G, Kowalczuk M, Jendrossek D: A new type of thermoalkalophilic hydrolase of Paucimonas lemoignei with high specificity for amorphous polyesters of short chain-length hydroxyalkanoic acids. J Biol Chem 2001, 276(39):36215–36224. 10.1074/jbc.M101106200View ArticlePubMedGoogle Scholar
- Handrick R, Reinhardt S, Kimmig P, Jendrossek D: The "intracellular" poly(3-hydroxybutyrate) (PHB) depolymerase of Rhodospirillum rubrum is a periplasm-located protein with specificity for native PHB and with structural similarity to extracellular PHB depolymerases. J Bacteriol 2004, 186(21):7243–7253. 10.1128/JB.186.21.7243-7253.2004PubMed CentralView ArticlePubMedGoogle Scholar
- Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, et al.: The Pfam protein families database. Nucleic Acids Res 2008, (36 Database):D281–288.Google Scholar
- Jaeger KE, Steinbüchel A, Jendrossek D: Substrate specificities of bacterial polyhydroxyalkanoate depolymerases and lipases: bacterial lipases hydrolyze poly(omega-hydroxyalkanoates). Appl Environ Microbiol 1995, 61(8):3113–3118.PubMed CentralPubMedGoogle Scholar
- Behrends A, Klingbeil B, Jendrossek D: Poly(3-hydroxybutyrate) depolymerases bind to their substrate by a C-terminal located substrate binding site. Fems Microbiol Lett 1996, 143(2–3):191–194. 10.1111/j.1574-6968.1996.tb08479.xView ArticlePubMedGoogle Scholar
- Handrick R, Reinhardt S, Jendrossek D: Mobilization of poly(3-hydroxybutyrate) in Ralstonia eutropha. J Bacteriol 2000, 182(20):5916–5918. 10.1128/JB.182.20.5916-5918.2000PubMed CentralView ArticlePubMedGoogle Scholar
- Pleiss J, Fischer M, Peiker M, Thiele C, Schmid RD: Lipase engineering database – Understanding and exploiting sequence-structure-function relationships. J Mol Catal B-Enzym 2000, 10(5):491–508. 10.1016/S1381-1177(00)00092-8View ArticleGoogle Scholar
- Fischer M, Pleiss J: The Lipase Engineering Database: a navigation and analysis tool for protein families. Nucleic Acids Research 2003, 31(1):319–321. 10.1093/nar/gkg015PubMed CentralView ArticlePubMedGoogle Scholar
- Fischer M, Thai QK, Grieb M, Pleiss J: DWARF – a data warehouse system for analyzing protein families. BMC Bioinformatics 2006, 7: 495. 10.1186/1471-2105-7-495PubMed CentralView ArticlePubMedGoogle Scholar
- Briese BH, Schmidt B, Jendrossek D: Pseudomonas lemoignei has five poly(hydroxyalkanoic acid) (PHA) depolymerase genes: a comparative study of bacterial and eucaryotic PHA depolymerases. J Environ Polym Degrad 1994, 2: 75–87. 10.1007/BF02074776View ArticleGoogle Scholar
- Brucato CL, Wong SS: Extracellular poly(3-hydroxybutyrate) depolymerase from Penicillium funiculosum: general characteristics and active site studies. Arch Biochem Biophys 1991, 290(2):497–502. 10.1016/0003-9861(91)90572-ZView ArticlePubMedGoogle Scholar
- de Eugenio LI, Garcia P, Luengo JM, Sanz JM, Roman JS, Garcia JL, Prieto MA: Biochemical evidence that phaZ gene encodes a specific intracellular medium chain length polyhydroxyalkanoate depolymerase in Pseudomonas putida KT2442: characterization of a paradigmatic enzyme. J Biol Chem 2007, 282(7):4951–4962. 10.1074/jbc.M608119200View ArticlePubMedGoogle Scholar
- Huisman GW, Wonink E, Meima R, Kazemier B, Terpstra P, Witholt B: Metabolism of poly(3-hydroxyalkanoates) (PHAs) by Pseudomonas oleovorans. Identification and sequences of genes and function of the encoded proteins in the synthesis and degradation of PHA. J Biol Chem 1991, 266(4):2191–2198.PubMedGoogle Scholar
- Jendrossek D, Backhaus M, Andermann M: Characterization of the Extracellular Poly(3-Hydroxybutyrate) Depolymerase of Comamonas Sp and of Its Structural Gene. Can J Microbiol 1995, 41: 160–169.View ArticlePubMedGoogle Scholar
- Jendrossek D, Muller B, Schlegel HG: Cloning and characterization of the poly(hydroxyalkanoic acid)-depolymerase gene locus, phaZ1, of Pseudomonas lemoignei and its gene product. Eur J Biochem 1993, 218(2):701–710. 10.1111/j.1432-1033.1993.tb18424.xView ArticlePubMedGoogle Scholar
- Kasuya KI, Inoue Y, Tanaka T, Akehata T, Iwata T, Fukui T, Doi Y: Biochemical and molecular characterization of the polyhydroxybutyrate depolymerase of Comamonas acidovorans YM isolated from freshwater. Appl Environ Microb 1609, 63(12):4844–4852.Google Scholar
- Kim DY, Kim HC, Kim SY, Rhee YH: Molecular characterization of extracellular medium-chain-length poly(3-hydroxyalkanoate) depolymerase genes from Pseudomonas alcaligenes strains. J Microbiol 2005, 43(3):285–294.PubMedGoogle Scholar
- Kita K, Mashiba S, Nagita M, Ishimaru K, Okamoto K, Yanase H, Kato N: Cloning of poly(3-hydroxybutyrate) depolymerase from a marine bacterium, Alcaligenes faecalis AE122, and characterization of its gene product. Biochim Biophys Acta 1997, 1352(1):113–122.View ArticlePubMedGoogle Scholar
- Klingbeil B, Kroppenstedt RM, Jendrossek D: Taxonomic identification of Streptomyces exfoliatus K10 and characterization of its poly(3-hydroxybutyrate) depolymerase gene. Fems Microbiol Lett 1996, 142(2–3):215–221. 10.1111/j.1574-6968.1996.tb08433.xView ArticlePubMedGoogle Scholar
- Kobayashi T, Sugiyama A, Kawase Y, Saito T, Mergaert J, Swings J: Biochemical and genetic characterization of an extracellular poly(3-hydroxybutyrate) depolymerase from Acidovorax sp strain TP4. J Environ Polym Degr 1999, 7(1):9–18. 10.1023/A:1021885901119View ArticleGoogle Scholar
- Ohura T, Kasuya KI, Doi Y: Cloning and characterization of the polyhydroxybutyrate depolymerase gene of Pseudomonas stutzeri and analysis of the function of substrate-binding domains. Appl Environ Microbiol 1999, 65(1):189–197.PubMed CentralPubMedGoogle Scholar
- Romen F, Reinhardt S, Jendrossek D: Thermotolerant poly(3-hydroxybutyrate)-degrading bacteria from hot compost and characterization of the PHB depolymerase of Schlegelella sp KB1a. Arch Microbiol 2004, 182(2–3):157–164.PubMedGoogle Scholar
- Saegusa H, Shiraki M, Kanai C, Saito T: Cloning of an intracellular Poly[D(-)-3-Hydroxybutyrate] depolymerase gene from Ralstonia eutropha H16 and characterization of the gene product. J Bacteriol 2001, 183(1):94–100. 10.1128/JB.183.1.94-100.2001PubMed CentralView ArticlePubMedGoogle Scholar
- Saito T, Suzuki K, Yamamoto J, Fukui T, Miwa K, Tomita K, Nakanishi S, Odani S, Suzuki J, Ishikawa K: Cloning, nucleotide sequence, and expression in Escherichia coli of the gene for poly(3-hydroxybutyrate) depolymerase from Alcaligenes faecalis. J Bacteriol 1989, 171(1):184–189.PubMed CentralPubMedGoogle Scholar
- Schirmer A, Jendrossek D: Molecular characterization of the extracellular poly(3-hydroxyoctanoic acid) [P(3HO)] depolymerase gene of Pseudomonas fluorescens GK13 and of its gene product. J Bacteriol 1994, 176(22):7065–7073.PubMed CentralPubMedGoogle Scholar
- Schober U, Thiel C, Jendrossek D: Poly(3-hydroxyvalerate) depolymerase of Pseudomonas lemoignei. Appl Environ Microbiol 2000, 66(4):1385–1392. 10.1128/AEM.66.4.1385-1392.2000PubMed CentralView ArticlePubMedGoogle Scholar
- Takaku H, Kimoto A, Kodaira S, Nashimoto M, Takagi M: Isolation of a Gram-positive poly(3-hydroxybutyrate) (PHB)-degrading bacterium from compost, and cloning and characterization of a gene encoding PHB depolymerase of Bacillus megaterium N-18–25–9. Fems Microbiology Letters 2006, 264(2):152–159. 10.1111/j.1574-6968.2006.00448.xView ArticlePubMedGoogle Scholar
- Takeda M, Kitashima K, Adachi K, Hanaoka Y, Suzuki I, Koizumi JI: Cloning and expression of the gene encoding thermostable poly(3-hydroxybutyrate) depolymerase. J Biosci Bioeng 2000, 90(4):416–421.View ArticlePubMedGoogle Scholar
- Jendrossek D, Handrick R: Diversität bakterieller PHB-Depolymerasen am Beispiel von Paucimonas gen. nov. lemoignei comb. nov. BIOspektrum 2001., 7:Google Scholar
- Tseng CL, Chen HJ, Shaw GC: Identification and characterization of the Bacillus thuringiensis phaZ gene, encoding new intracellular poly-3-hydroxybutyrate depolymerase. J Bacteriol 2006, 188(21):7592–7599. 10.1128/JB.00729-06PubMed CentralView ArticlePubMedGoogle Scholar
- Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL: GenBank. Nucleic Acids Res 2007, (35 Database):D21–25. 10.1093/nar/gkl986
- Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389–3402. 10.1093/nar/25.17.3389PubMed CentralView ArticlePubMedGoogle Scholar
- Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res 2000, 28(1):235–242. 10.1093/nar/28.1.235PubMed CentralView ArticlePubMedGoogle Scholar
- Kabsch W, Sander C: Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22(12):2577–2637. 10.1002/bip.360221211View ArticlePubMedGoogle Scholar
- Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22(22):4673–4680. 10.1093/nar/22.22.4673PubMed CentralView ArticlePubMedGoogle Scholar
- Abe T, Kobayashi T, Saito T: Properties of a novel intracellular poly(3-hydroxybutyrate) depolymerase with high specific activity (PhaZd) in Wautersia eutropha H16. Journal of Bacteriology 2005, 187(20):6982–6990. 10.1128/JB.187.20.6982-6990.2005PubMed CentralView ArticlePubMedGoogle Scholar
- Fischer M, Knoll M, Sirim D, Wagner F, Funke S, Pleiss J: The Cytochrome P450 Engineering Database: a navigation and prediction tool for the cytochrome P450 protein family. Bioinformatics 2007, 23(15):2015–2017. 10.1093/bioinformatics/btm268View ArticlePubMedGoogle Scholar
- Knoll M, Pleiss J: The Medium-Chain Dehydrogenase/Reductase Engineering Database: A systematic analysis of a diverse protein family to understand sequence-structure-function relationship. Protein Sci 2008, 17: 1689–1697. 10.1110/ps.035428.108PubMed CentralView ArticlePubMedGoogle Scholar
- Rice P, Longden I, Bleasby A: EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 2000, 16(6):276–277. 10.1016/S0168-9525(00)02024-2View ArticlePubMedGoogle Scholar
- Jendrossek D, Frisse A, Behrends A, Andermann M, Kratzin HD, Stanislawski T, Schlegel HG: Biochemical and molecular characterization of the Pseudomonas lemoignei polyhydroxyalkanoate depolymerase system. J Bacteriol 1995, 177(3):596–607.PubMed CentralPubMedGoogle Scholar
- Hisano T, Kasuya K, Tezuka Y, Ishii N, Kobayashi T, Shiraki M, Oroudjev E, Hansma H, Iwata T, Doi Y, et al.: The crystal structure of polyhydroxybutyrate depolymerase from Penicillium funiculosum provides insights into the recognition and degradation of biopolyesters. J Mol Biol 2006, 356(4):993–1004. 10.1016/j.jmb.2005.12.028View ArticlePubMedGoogle Scholar
- Papageorgiou AC, Hermawan S, Singh CB, Jendrossek D: Structural basis of poly(3-hydroxybutyrate) hydrolysis by PhaZ7 depolymerase from Paucimonas lemoignei. J Mol Biol 2008, 382(5):1184–1194. 10.1016/j.jmb.2008.07.078View ArticlePubMedGoogle Scholar
- Takaku H, Kimoto A, Kodaira S, Nashimoto M, Takagi M: Isolation of a Gram-positive poly(3-hydroxybutyrate) (PHB)-degrading bacterium from compost, and cloning and characterization of a gene encoding PHB depolymerase of Bacillus megaterium N-18–25–9. Fems Microbiol Lett 2006, 264(2):152–159. 10.1111/j.1574-6968.2006.00448.xView ArticlePubMedGoogle Scholar
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