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

By Michael Knoll, Thomas M Hamm, Florian Wagner, Virginia Martinez and Jürgen Pleiss
Topics: Database
Publisher: BioMed Central
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Provided by: PubMed Central

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  2. (1999). Biochemical and genetic characterization of an extracellular poly(3-hydroxybutyrate) depolymerase from Acidovorax sp strain TP4. J Environ Polym Degr
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  5. (2000). Bleasby A: EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet
  6. (2004). Calabia BP: Degradation of microbial polyesters.
  7. (1995). Characterization of the Extracellular Poly(3-Hydroxybutyrate) Depolymerase of Comamonas Sp and of Its Structural Gene.
  8. (1999). Cloning and characterization of the polyhydroxybutyrate depolymerase gene of Pseudomonas stutzeri and analysis of the function of substrate-binding domains. Appl Environ Microbiol
  9. (2000). Cloning and expression of the gene encoding thermostable poly(3-hydroxybutyrate) depolymerase.
  10. (2001). Cloning of an intracellular Poly[D(-)-3-Hydroxybutyrate] depolymerase gene from Ralstonia eutropha H16 and characterization of the gene product.
  11. (1989). Cloning, nucleotide sequence, and expression in Escherichia coli of the gene for poly(3-hydroxybutyrate) depolymerase from Alcaligenes faecalis.
  12. (1990). Dawes EA: Occurrence, metabolism, metabolic role, and industrial uses of bacterial polyhydroxyalkanoates. Microbiol Rev
  13. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers
  14. (2001). Diversität bakterieller PHBDepolymerasen am Beispiel von Paucimonas gen. nov. lemoignei comb. nov. BIOspektrum
  15. (2006). DWARF – a data warehouse system for analyzing protein families.
  16. (2007). From oil to bioplastics, a dream come true?
  17. (2006). GC: Identification and characterization of the Bacillus thuringiensis phaZ gene, encoding new intracellular poly-3-hydroxybutyrate depolymerase.
  18. (2002). Handrick R: Microbial degradation of polyhydroxyalkanoates. Annu Rev Microbiol
  19. (1995). HG: Biochemical and molecular characterization of the Pseudomonas lemoignei polyhydroxyalkanoate depolymerase system.
  20. (1993). HG: Cloning and characterization of the poly(hydroxyalkanoic acid)-depolymerase gene locus, phaZ1, of Pseudomonas lemoignei and its gene product.
  21. (2006). 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
  22. (2006). 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
  23. (1994). Jendrossek D: Molecular characterization of the extracellular poly(3-hydroxyoctanoic acid) [P(3HO)] depolymerase gene of Pseudomonas fluorescens GK13 and of its gene product.
  24. (1995). Jendrossek D: Substrate specificities of bacterial polyhydroxyalkanoate depolymerases and lipases: bacterial lipases hydrolyze poly(omega-hydroxyalkanoates). Appl Environ Microbiol
  25. (1997). Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res
  26. (1999). Luengo JM: Novel biodegradable aromatic plastics from a bacterial source – Genetic and biochemical studies on a route of the phenylacetyl-CoA catabolon.
  27. (1991). 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.
  28. (2000). Mobilization of poly(3-hydroxybutyrate) in Ralstonia eutropha.
  29. (1997). N: Cloning of poly(3-hydroxybutyrate) depolymerase from a marine bacterium, Alcaligenes faecalis AE122, and characterization of its gene product. Biochim Biophys Acta
  30. (2000). PE: The Protein Data Bank. Nucleic Acids Res
  31. (1996). Poly(3-hydroxybutyrate) depolymerases bind to their substrate by a C-terminal located substrate binding site. Fems Microbiol Lett
  32. (2000). Poly(3-hydroxyvalerate) depolymerase of Pseudomonas lemoignei.
  33. (1994). Pseudomonas lemoignei has five poly(hydroxyalkanoic acid) (PHA) depolymerase genes: a comparative study of bacterial and eucaryotic PHA depolymerases. J Environ Polym Degrad
  34. (2000). RD: Lipase engineering database – Understanding and exploiting sequencestructure-function relationships. J Mol Catal B-Enzym
  35. (2008). Structural basis of poly(3-hydroxybutyrate) hydrolysis by PhaZ7 depolymerase from Paucimonas lemoignei.
  36. (1996). Taxonomic identification of Streptomyces exfoliatus K10 and characterization of its poly(3-hydroxybutyrate) depolymerase gene. Fems Microbiol Lett
  37. (2004). 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.
  38. (2006). The crystal structure of polyhydroxybutyrate depolymerase from Penicillium funiculosum provides insights into the recognition and degradation of biopolyesters.
  39. (2007). The Cytochrome P450 Engineering Database: a navigation and prediction tool for the cytochrome P450 protein family. Bioinformatics
  40. (2003). The Lipase Engineering Database: a navigation and analysis tool for protein families. Nucleic Acids Research
  41. (2008). The Medium-Chain Dehydrogenase/Reductase Engineering Database: A systematic analysis of a diverse protein family to understand sequence-structure-function relationship. Protein Sci
  42. The Pfam protein families database.
  43. (2004). Thermotolerant poly(3-hydroxybutyrate)-degrading bacteria from hot compost and characterization of the PHB depolymerase of Schlegelella sp KB1a. Arch Microbiol
  44. (1994). 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
  45. (1991). Wong SS: Extracellular poly(3-hydroxybutyrate) depolymerase from Penicillium funiculosum: general characteristics and active site studies. Arch Biochem Biophys
  46. (2005). YH: Molecular characterization of extracellular medium-chain-length poly(3-hydroxyalkanoate) depolymerase genes from Pseudomonas alcaligenes strains.

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