Novel biocatalysis by database mining

Current Opinion in Biotechnology

Volumn 15, Issue 4, 2004, Pages 280-284

  Wackett, Lawrence P ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME VARIANT; REAGENT;

ANALOG COMPUTER; BIOCATALYST; BIOSYNTHESIS; BIOTECHNOLOGY; CATALYSIS; DATA BASE; ENANTIOSELECTIVITY; INFORMATION; MINING; PRIORITY JOURNAL; REVIEW; SYNTHESIS; UNITED STATES;

CATALYSIS; CHEMICAL INDUSTRY; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; DRUG DESIGN; ENZYMES; INFORMATION STORAGE AND RETRIEVAL; PROTEIN ENGINEERING; SEQUENCE ANALYSIS, PROTEIN;

EID: 3543120144     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.copbio.2004.05.003     Document Type: Review

References (35)

1. Ball P: The Ingredients: a Guided Tour of the Elements. Oxford: Oxford Press; 2003.
2. Smith MB, March J: March's Advanced Organic Chemistry: Reactions, Mechanisms, and Structure, edn 5. New York: Wiley & Sons; 2001.
3. Patai S: Patai's Guide to the Chemistry of Functional Groups. New York: Wiley & Sons; 1989.
4. Fieser LF, Fieser M: Fieser's Reagents for Organic Synthesis, Volumes 1-12. New York: Wiley & Sons; 1990.
5. Faber K: Biotransformations in Organic Chemistry, edn 4. Berlin: Springer Verlag; 2000.
6. Davis J.K., Paoli G.C., He Z., Nadeau L.J., Somerville C.C., Spain J.C. Sequence analysis and initial characterization of two isozymes of hydroxylaminobenzene mutase from Pseudomonas pseudoalcaligenes JS45. Appl Environ Microbiol. 66:2000;2965-2971
7. Kato Y., Nakamura K., Sakiyama H., Mayhew S.G., Asano Y. Novel heme-containing lyase, phenylacetaldoxime dehydratase from Bacillus sp. strain OxB-1: purification, characterization, and molecular cloning of the gene. Biochemistry. 39:2000;800-809
8. Yeung K.F., Lee K.M., Woodard R.W. Isolation and identification of two L-azetidine-2-carboxylic acid-degrading soil microorganisms, Enterobacter agglomerans and Enterobacter amnigenus. J Nat Prod. 61:1998;207-211
9. Krieger C.J., Roseboom W., Albracht S.P., Spormann A.M. A stable organic free radical in anaerobic benzylsuccinate synthase of Azoarcus sp. strain T. J Biol Chem. 276:2001;12924-12927
10. Negrete-Raymond A.C., Weder B., Wackett L.P. Catabolism of arylboronic acids by Arthrobacter nicotinovorans strain PBA. Appl Environ Microbiol. 69:2003;4263-4267
11. Pak J.W., Knoke K.L., Noguera D.R., Fox B.G., Chambliss G.H. Transformation of 2,4,6-trinitrotoluene by purified xenobiotic reductase B from Pseudomonas fluorescens I-C. Appl Environ Microbiol. 66:2000;4742-4750
12. Fowden L. Azetidine-2-carboxylic acid: a new cyclic imino acid occurring in plants. Biochem J. 64:1956;323-332
13. Wackett LP, Hershberger CD: Biocatalysis and Biodegradation: Microbial Transformation of Organic Compounds. Washington, DC: American Society for Microbiology Press; 2001.
14. Gray K.A., Richardson T.H., Robertson D.E., Swanson P.E., Subramanian M.V. Soil-based gene discovery: a new technology to accelerate and broaden biocatalytic applications. Adv Appl Microbiol. 52:2003;1-27 This review compiles information on a range of approaches for engineering novel biocatalytic processes. It illustrates how metagenome screening, directed evolution and rational design approaches can be combined for powerful effect.
15. Weightman A.J., Weightman A.L., Slater J.H. Stereospecificity of 2-monochloropropionate dehalogenation by the two dehalogenases of Pseudomonas putida PP3: evidence for two different dehalogenation mechanisms. J Gen Microbiol. 128:1982;1755-1762
16. Swanson P.E. Dehalogenases applied to industrial-scale biocatalysis. Curr Opin Biotechnol. 10:1999;365-369
17. Verschueren K.H., Seljee F., Rozeboom H.J., Kalk K.H., Dijkstra B.W. Crystallographic analysis of the catalytic mechanism of haloalkane dehalogenase. Nature. 363:1993;693-698
18. Newman J., Peat T.S., Richard R., Kan L., Swanson P.E., Affholter J.A., Holmes I.H., Schindler J.F., Unkefer C.J., Terwilliger T.C. Haloalkane dehalogenases: structure of a Rhodococcus enzyme. Biochemistry. 38:1999;16105-16114
19. Ellis L.B.M., Hou B.K., Kang W., Wackett L.P. The University of Minnesota Biocatalysis/Biodegradation Database: post genomic data mining. Nucleic Acids Res. 31:2003;262-265 The biocatalysis/biodegradation database focuses on novel reactions useful for environmental and industrial biotechnology. The development of new functionality to predict reactions is described.
20. Schomburg I., Chang A., Ebeling C., Gremse M., Heldt C., Huhn G., Schomburg D. BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Res. 32:2004;D431-D433 The BRENDA database offers the most comprehensive freely available resource for obtaining information on the substrate specificity, regiospecificity and enantioselectivity of enzymes. This review highlights recent developments.
21. Goto S., Okuno Y., Hattori M., Nishioka T., Kanehisa M. LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Res. 30:2002;402-404
22. Lee P.C., Momen A.Z., Mijts B.N., Schmidt-Dannert C. Biosynthesis of structurally novel carotenoids in Escherichia coli. Chem Biol. 10:2003;453-462
23. 12-dependent glycerol dehydratase- and diol dehydratase-encoding genes from metagenomic DNA libraries derived from enrichment cultures. Appl Environ Microbiol. 69:2003;3048-3060
24. Kanehisa M., Goto S., Kawashima S., Okuno Y., Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res. 32:2004;D277-D280
25. Krieger C.J., Zhang P., Mueller L.A., Wang A., Paley S., Arnaud M., Pick J., Rhee S.Y., Karp P.D. MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 32:2004;D438-D442 The MetaCyc database provides well-curated information on metabolic pathways from microbes and plants. This review describes the expansion of the database into its current form.
26. Wackett LP: Applications of genomics to biocatalysis and biodegradation. In Microbial Genomes. Edited by Fraser CM, Read T, Nelson KE: Totowa, New Jersey: The Human Press, Inc; 2004: 443-459.
27. Hou B.K., Wackett L.P., Ellis L.B.M. Microbial pathway prediction: a functional group approach. J Chem Inf Comp Sci. 43:2003;1051-1057 This paper describes the construction of a freely available software tool for predicting enzymatic transformations of any chemical compound drawn by the user. The tool is based on metabolic rules and thus can be used to predict metabolic pathways that could be engineered for biocatalytic purposes.
28. Rouhi A.M. Chiral business. Chem Eng News. 81:2003;45-55
29. Wada M., Hsu C.C., Franke D., Mitchell M., Heine A., Wilson I., Wong C.H. Directed evolution of N-acetylneuraminic acid aldolase to catalyze enantiomeric aldol reactions. Bioorg Med Chem. 11:2003;2091-2098
30. Williams G.J., Domann S., Nelson A., Berry A. Modifying the stereochemistry of an enzyme-catalyzed reaction by directed evolution. Proc Natl Acad Sci USA. 100:2003;3143-3148
31. Bocola M., Otte N., Jaeger K.E., Reetz M.T., Thiel W. Learning from directed evolution: theoretical investigations into cooperative mutations in lipase enantioselectivity. Chembiochem. 5:2004;214-223
32. Palackal N., Brennan Y., Callen W.N., Dupree P., Frey G., Goubet F., Hazlewood G.P., Healey S., Kang Y.E., Kretz K.A., et al. An evolutionary route to xylanase process fitness. Protein Sci. 13:2004;494-503
33. Voget S., Leggewie C., Uesbeck A., Raasch C., Jaeger K.E., Streit W.R. Prospecting for novel biocatalysts in a soil metagenome. Appl Environ Microbiol. 69:2003;6235-6242
34. Gouverneur V.E., Houk K.N., de Pascual-Teresa B., Beno B., Janda K.D., Lerner R.A. Control of the exo and endo pathways of the Diels-Alder reaction by antibody catalysis. Science. 262:1993;204-208
35. Ose T., Watanabe K., Mie T., Honma M., Watanabe H., Yao M., Oikawa H., Tanaka I. Insight into a natural Diels-Alder reaction from the structure of macrophomate synthase. Nature. 422:2003;185-189 Diels-Alder reactions are very important in organic synthesis, particularly in the synthesis of pharmaceuticals. This paper describes the elucidation of the high-resolution structure of an enzyme catalyzing Diels-Alder reactions and shows it has a large, hydrophobic active site that may be amenable to protein engineering.