Improvement of the fungal enzyme pyranose 2-oxidase using protein engineering

Journal of Biotechnology

Volumn 124, Issue 1, 2006, Pages 26-40

  Heckmann Pohl, Dorothée M ^a   Bastian, Sabine ^a   Altmeier, Silke ^a   Antes, Iris ^b  

^a SAARLAND UNIVERSITY   (Germany)

^b MAX PLANCK INSTITUTE FOR INFORMATICS   (Germany)

Author keywords

Bioconversion; Enzyme ligand interactions; Improved enzyme variants; Molecular docking; Pyranose 2 oxidase gene; Rational protein design; Structure activity relationship

Indexed keywords

CATALYSIS; FUNGI; GENES; HYDROGEN BONDS; PH EFFECTS; PROTEINS; X RAY ANALYSIS;

ENZYME-LIGAND INTERACTIONS; IMPROVED ENZYME VARIANTS; MOLECULAR DOCKING; PYRANOSE 2-OXIDASE GENE; RATIONAL PROTEIN DESIGN; STRUCTURE-ACTIVITY RELATIONSHIP;

ENZYMES;

CARBOHYDRATE; ENZYME; FUNGAL ENZYME; GLUCOSE; PYRANOSE 2 OXIDASE; SELENOMETHIONINE; SORBOSE; UNCLASSIFIED DRUG; XYLOSE;

AMINO ACID SUBSTITUTION; ARTICLE; BIOTRANSFORMATION; CALCULATION; CARBOXY TERMINAL SEQUENCE; CATALYSIS; CRYSTAL STRUCTURE; ENZYME ANALYSIS; ENZYME SPECIFICITY; ESCHERICHIA COLI; FUNGUS; GENE EXPRESSION; HYDROGEN BOND; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; OXYGEN SATURATION; PENIOPHORA; PH; PRIORITY JOURNAL; PROTEIN ENGINEERING; PROTEIN INTERACTION; STRUCTURE ACTIVITY RELATION; X RAY ANALYSIS;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; BASE SEQUENCE; BASIDIOMYCOTA; BINDING SITES; CARBOHYDRATE DEHYDROGENASES; CATALYSIS; CRYSTALLOGRAPHY, X-RAY; ENZYME STABILITY; ESCHERICHIA COLI; FUNGAL PROTEINS; HEAT; HISTIDINE; HYDROGEN-ION CONCENTRATION; KINETICS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; OXIDATION-REDUCTION; PHYLOGENY; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN ENGINEERING; RECOMBINANT PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY; VARIATION (GENETICS);

ESCHERICHIA COLI; PENIOPHORA;

EID: 33744538494     PISSN: 01681656     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2006.02.003     Document Type: Article

References (45)

1. Albrecht M., and Lengauer T. Pyranose oxidase identified as member of the GMC oxidoreductase family. Bioinformatics 1 (2003) 1-5
2. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3401
3. Bannwarth M., Bastian S., Heckmann-Pohl D., Giffhorn F., and Schulz G.E. Crystal structure of pyranose 2-oxidase from the white-rot fungus Peniophora sp. Biochemistry 43 (2004) 11683-11690
4. Bannwarth, M., Heckmann-Pohl, D., Bastian, S., Giffhorn, F., Schulz, G.E. Reaction geometry and thermostable variant of pyranose 2-oxidase from the white-rot fungus Peniophora sp. Biochemistry, submitted for publication.
5. Bastian S., Rekowski M.J., Witte K., Heckmann-Pohl D.M., and Giffhorn F. Engineering of pyranose 2-oxidase from Peniophora gigantea towards improved thermostability and catalytic efficiency. Appl. Microbiol. Biotechnol. 67 (2005) 654-663
6. Baute M.A., Baute M.R., and Deffieux M.G. Proposed pathway to the pyrones cortalcerone and microthecin in fungi. Phytochemistry 26 (1987) 1395-1397
7. Bornscheuer U.T., and Pohl M. Improved biocatalysts by directed evolution and rational protein design. Curr. Opin. Chem. Biol. 5 (2001) 137-143
8. Bungert D., Bastian S., Heckmann-Pohl D.M., Giffhorn F., Heinzle E., and Tholey A. Screening of sugar converting enzymes using quantitative MALDI-ToF mass spectrometry. Biotechnol. Lett. 26 (2004) 1025-1030
9. Cavener D.R. GMC oxidoreductases. A newly defined family of homologous proteins with diverse catalytic activities. J. Mol. Biol. 223 (1992) 811-814
10. Christensen, S., Lassen, S.F., Schneider, P., 2000. Nucleic acids encoding polypeptides having pyranose oxidase activity. US Patent 6,146,865.
11. 2 during wood degradation by Phanerochaete chrysosporium, Trametes versicolor, and Oudemansiella mucida. Appl. Environ. Microbiol. 60 (1994) 2524-2532
12. Danneel H.J., Rössner E., Zeeck A., and Giffhorn F. Purification and characterization of a pyranose oxidase from the basidiomycete Peniophora gigantea and chemical analysis of its reaction products. Eur. J. Biochem. 214 (1993) 795-802
13. de Koker T.H., Mozuch M.D., Cullen D., Gaskell J., and Kersten P.J. Isolation and purification of pyranose 2-oxidase from Phanerochaete chrysosporium and characterization of gene structure and regulation. Appl. Environ. Micobiol. 70 (2004) 5794-5800
14. Eijsink V.G.H., Bjork A., Gaseidnes S., Sirevag R., Synstad B., van den Burg B., and Vriend G. Rational engineering of enzyme stability. J. Biotechnol. 113 (2004) 105-120
15. Flannery A.V., Beynon R.J., and Bond J.S. Proteolysis of proteins for sequencing analysis and peptide mapping. In: Beynon R.J., and Bond J.S. (Eds). Proteolytic Enzymes: A Practical Approach (1989), IRL Press, Oxford, UK
16. Freimund S., Giffhorn F., Huwig A., and Köpper S. Rare keto-aldoses from enzymatic oxidation: substrates and oxidation products of pyranose oxidase. Chem. Eur. J. 4 (1998) 2442-2455
17. Giffhorn F. Fungal pyranose oxidase: occurrence, properties and biotechnical applications in carbohydrate chemistry. Mini review. Appl. Microbiol. Biotechnol. 54 (2000) 727-740
18. Guex N., and Peitsch M.C. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18 (1997) 2714-2723
19. Halada P., Leitner C., Sedmera P., Haltrich D., and Volc J. Identification of the covalent flavine adenine dinucleotide-binding region in pyranose 2-oxidase from Trametes multicolor. Anal. Biochem. 314 (2003) 235-242
20. Hallberg B.M., Leitner C., Haltrich D., and Divne C. Crystal structure of the 270 kDa homotetrameric lignin-degrading enzyme pyranose 2-oxidase. J. Mol. Biol. 341 (2004) 781-796
21. Hopwood D.A., Bibb M.J., Chater K.F., Kieser T., Bruton C.J., Kieser D.J., Lydiate D.J., Smith C.P., Ward J.M., and Schrempf H. Genetic Manipulation of Streptomyces: A Laboratory Manual (1985), The John Innes Foundation, Norwich, UK
22. Humphrey W., Dalke A., and Schulten K. VMD-visual molecular dynamics. J. Mol. Graph. 14 (1996) 33-38
23. Kuchner O., and Arnold F.H. Directed evolution of enzyme catalysts. Trends Biotechnol. 15 (1997) 523-530
24. Leitner C., Volc J., and Haltrich D. Purification and characterization of pyranose oxidase from the white rot fungus Trametes multicolor. Appl. Environ. Microbiol. 67 (2001) 3636-3644
25. Leung D.W., Chen E.Y., and Goeddel D.V. A method for random mutagenesis of a defined DNA segment using a modified polymerase chain reaction. Technique 1 (1989) 11-15
26. Marešová H., Večerek B., Hradská M., Libessart N., Bečka S., Saniez M.-H., and Kyslík P. Expression of the pyranose 2-oxidase from Trametes pubescens in Escherichia coli and characterization of the recombinant enzyme. J. Biotechnol. 120 (2005) 387-395
27. Masuda-Nishimura I., Minamihara T., and Koyama Y. Improvement in thermal stability and reactivity of pyranose oxidase from Coriolus versicolor by random mutagenesis. Biotechnol. Lett. 21 (1999) 203-207
28. Meyer M., Wohlfahrt G., Knablein J., and Schomburg D. Aspects of the mechanism of catalysis of glucose oxidase: a docking, molecular mechanics and quantum chemical study. J. Comput. Aided Mol. Des. 12 (1998) 425-440
29. Minagawa H., Nakayama N., and Nakamoto S. Thermostabilization of lactate oxidase by random mutagenesis. Biotechnol. Lett. 17 (1995) 975-980
30. Nishimura I., Okada K., and Koyama Y. Cloning and expression of pyranose oxidase cDNA from Coriolus versicolor in Escherichia coli. J. Biotechnol. 52 (1996) 11-20
31. Nishimura I., Okada K., Minamihara T., Kawai G., Koyama Y., and Suzuki M. Pyranose oxidase, pyranose oxidase gene, novel recombinant DNA and process for producing pyranose oxidase (1998), Kikkoman Corporation, Noda, Japan US Patent 5,712,139
32. Pearson W.R., and Lipman D.J. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. U.S.A. 85 (1988) 2444-2448
33. Pugsley A.P. The complete general secretory pathway in Gram-negative bacteria. Microbiol. Rev. 57 (1993) 50-108
34. Rarey M., Kramer B., and Lengauer T. Multiple automatic base selection: Protein-ligand docking based on incremental construction without manual intervention. J. Comput. Aided Mol. Des. 11 (1997) 369-384
35. Sambrook J., Fritsch E.F., and Maniatis T. Molecular Cloning: A Laboratory Manual. second ed. (1989), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
36. Schäfer A., Bieg S., Huwig A., Kohring G.W., and Giffhorn F. Purification by immunoaffinity chromatography, characterization, and structural analysis of a thermostable pyranose oxidase from the white rot fungus Phlebiopsis gigantea. Appl. Environ. Microbiol. 62 (1996) 2586-2592
37. Takakura Y., and Kuwata S. Purification, characterization, and molecular cloning of a pyranose oxidase from the fruit body of the basidiomycete Tricholoma matsutake. Biosci. Biotechnol. Biochem. 67 (2003) 2598-2607
38. Treitz G., Maria G., Giffhorn F., and Heinzle E. Kinetic model discrimination via step-by-step experimental and computational procedure in the enzymatic oxidation of d-glucose. J. Biotechnol. 85 (2001) 271-287
39. Večerek B., Marešová H., Kočanová M., and Kyslík P. Molecular cloning and expression of the pyranose 2-oxidase cDNA from Trametes ochracea MB49 in Escherichia coli. Appl. Microbiol. Biotechnol. 64 (2004) 525-530
40. Vielle C., and Zeikus G.J. Hyperthermophilic enzymes: sources, uses, and molecular mechanism for thermostability. Microbiol. Mol. Biol. Rev. 65 (2001) 1-43
41. Volc J., Kubátová E., Sedmera P., Daniel G., and Gabriel J. Pyranose oxidase and pyranosone dehydratase: enzymes responsible for conversion of d-glucose to cortalcerone by the basidiomycete Phanerochaete chrysosporium. Arch. Microbiol. 156 (1991) 297-301
42. Volc J., Sedmera P., Halada P., Dwivedi P., and Costa Ferreira M. Conversion of d-galactose to d-threo-hexos-2,3-diulose by fungal pyranose oxidase. J. Carbohydr. Chem. 22 (2003) 207-216
43. Wierenga R.K., Terpstra P., and Hol W.G.J. Prediction of the occurrence of the ADP-binding βαβ-fold in proteins, using an amino acid sequence fingerprint. J. Mol. Biol. 187 (1986) 101-107
44. Wohlfahrt G., Witt S., Hendle J., Schomburg D., Kalisz H.M., and Hecht H.J. 1.8 and 1.9 Å resolution structures of the Penicillium amagasakiense and Aspergillus niger glucose oxidases as a basis for modelling substrate complexes. Acta Crystallogr. D Biol. Crystallogr. 55 (1999) 969-977
45. Yamada H., Mori N., and Tani Y. Properties of choline oxidase of Cylindrocarpon didymum M-1. Agric. Biol. Chem. 43 (1979) 2173-2177