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Volumn 1764, Issue 7, 2006, Pages 1159-1166

Improving the catalytic efficiency of a meta-cleavage product hydrolase (CumD) from Pseudomonas fluorescens IP01

Author keywords

Cumene degradation; Meta cleavage product hydrolase; Polychlorinated biphenyl degradation; Site directed mutagenesis; Substrate specificity; X ray crystallography

Indexed keywords

2 HYDROXY 6 OXOHEPTA 2,4 DIENOATE; AMINO ACID; AROMATIC COMPOUND; CHLORIDE; CUMENE; HYDROLASE; HYDROXYL GROUP; MUTANT PROTEIN; OXYGEN; SERINE; UNCLASSIFIED DRUG;

EID: 33746033393     PISSN: 15709639     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbapap.2006.05.010     Document Type: Article
Times cited : (4)

References (40)
  • 2
    • 0035729093 scopus 로고    scopus 로고
    • Bacterial degradation of aromatic compounds via angular dioxygenation
    • Nojiri H., Habe H., and Omori T. Bacterial degradation of aromatic compounds via angular dioxygenation. J. Gen. Appl. Microbiol. 47 (2001) 279-305
    • (2001) J. Gen. Appl. Microbiol. , vol.47 , pp. 279-305
    • Nojiri, H.1    Habe, H.2    Omori, T.3
  • 3
    • 0000843661 scopus 로고    scopus 로고
    • Molecular bases of aerobic bacterial degradation of dioxins: involvement of angular dioxygenation
    • Nojiri H., and Omori T. Molecular bases of aerobic bacterial degradation of dioxins: involvement of angular dioxygenation. Biosci. Biotechnol. Biochem. 66 (2002) 2001-2016
    • (2002) Biosci. Biotechnol. Biochem. , vol.66 , pp. 2001-2016
    • Nojiri, H.1    Omori, T.2
  • 4
    • 0037506334 scopus 로고    scopus 로고
    • Genetics of polycyclic aromatic hydrocarbon metabolism in diverse aerobic bacteria
    • Habe H., and Omori T. Genetics of polycyclic aromatic hydrocarbon metabolism in diverse aerobic bacteria. Biosci. Biotechnol. Biochem. 67 (2003) 225-243
    • (2003) Biosci. Biotechnol. Biochem. , vol.67 , pp. 225-243
    • Habe, H.1    Omori, T.2
  • 5
    • 0000976639 scopus 로고
    • Biochemistry of aromatic hydrocarbon degradation in Pseudomonads
    • Sokatch J.R., and Ornston L.N. (Eds), Academic Press, New York
    • Dagley S. Biochemistry of aromatic hydrocarbon degradation in Pseudomonads. In: Sokatch J.R., and Ornston L.N. (Eds). The Bacteria (1986), Academic Press, New York 527-555
    • (1986) The Bacteria , pp. 527-555
    • Dagley, S.1
  • 7
    • 0025935159 scopus 로고
    • Aromatic hydrocarbon degradation: a molecular approach
    • Setlow J.K. (Ed), Plenum Press, New York
    • Zylstra G.J., and Gibson D.T. Aromatic hydrocarbon degradation: a molecular approach. In: Setlow J.K. (Ed). Genetic Engineering (1991), Plenum Press, New York 183-203
    • (1991) Genetic Engineering , pp. 183-203
    • Zylstra, G.J.1    Gibson, D.T.2
  • 8
    • 0018306487 scopus 로고
    • Effect of chlorine substitution on the bacterial metabolism of various polychlorinated biphenyls
    • Furukawa K., Tomizuka N., and Kamibayashi A. Effect of chlorine substitution on the bacterial metabolism of various polychlorinated biphenyls. Appl. Environ. Microbiol. 38 (1979) 301-310
    • (1979) Appl. Environ. Microbiol. , vol.38 , pp. 301-310
    • Furukawa, K.1    Tomizuka, N.2    Kamibayashi, A.3
  • 9
    • 0027223958 scopus 로고
    • Gene components responsible for discrete substrate specificity in the metabolism of biphenyl (bph operon) and toluene (tod operon)
    • Furukawa K., Hirose J., Suyama A., Zaiki T., and Hayashida S. Gene components responsible for discrete substrate specificity in the metabolism of biphenyl (bph operon) and toluene (tod operon). J. Bacteriol. 175 (1993) 5224-5232
    • (1993) J. Bacteriol. , vol.175 , pp. 5224-5232
    • Furukawa, K.1    Hirose, J.2    Suyama, A.3    Zaiki, T.4    Hayashida, S.5
  • 10
    • 0025697216 scopus 로고
    • Influence of chlorine substitution pattern on the degradation of polychlorinated biphenyls by eight bacterial strains
    • Bedard D.L., and Haberl M.L. Influence of chlorine substitution pattern on the degradation of polychlorinated biphenyls by eight bacterial strains. Microb. Ecol. 20 (1990) 87-102
    • (1990) Microb. Ecol. , vol.20 , pp. 87-102
    • Bedard, D.L.1    Haberl, M.L.2
  • 11
    • 0029032311 scopus 로고
    • Conversion of chlorobiphenyls into phenylhexadienoates and benzoates by the enzymes of the upper pathway for polychlorobiphenyl degradation encoded by the bph locus of Pseudomonas sp. strain LB400
    • Seeger M., Timmis K.N., and Hofer B. Conversion of chlorobiphenyls into phenylhexadienoates and benzoates by the enzymes of the upper pathway for polychlorobiphenyl degradation encoded by the bph locus of Pseudomonas sp. strain LB400. Appl. Environ. Microbiol. 61 (1995) 2654-2658
    • (1995) Appl. Environ. Microbiol. , vol.61 , pp. 2654-2658
    • Seeger, M.1    Timmis, K.N.2    Hofer, B.3
  • 12
    • 0035110711 scopus 로고    scopus 로고
    • Comparative specificities of two evolutionarily divergent hydrolases involved in microbial degradation of polychlorinated biphenyls
    • Seah S.Y.K., Labbe G., Kaschabek S.R., Reifenrath F., Reineke W., and Eltis L.D. Comparative specificities of two evolutionarily divergent hydrolases involved in microbial degradation of polychlorinated biphenyls. J. Bacteriol. 183 (2001) 1511-1516
    • (2001) J. Bacteriol. , vol.183 , pp. 1511-1516
    • Seah, S.Y.K.1    Labbe, G.2    Kaschabek, S.R.3    Reifenrath, F.4    Reineke, W.5    Eltis, L.D.6
  • 13
    • 0034717267 scopus 로고    scopus 로고
    • Identification of a serine hydrolase as a key determinant in the microbial degradation of polychlorinated biphenyls
    • Seah S.Y.K., Labbe G., Nerdinger S., Johnson M.R., Snieckus V., and Eltis L.D. Identification of a serine hydrolase as a key determinant in the microbial degradation of polychlorinated biphenyls. J. Biol. Chem. 275 (2000) 15701-15708
    • (2000) J. Biol. Chem. , vol.275 , pp. 15701-15708
    • Seah, S.Y.K.1    Labbe, G.2    Nerdinger, S.3    Johnson, M.R.4    Snieckus, V.5    Eltis, L.D.6
  • 14
    • 0032483324 scopus 로고    scopus 로고
    • Purification and preliminary characterization of a serine hydrolase involved in the microbial degradation of polychlorinated biphenyls
    • Seah S.Y.K., Terracina G., Bolin J.T., Riebel P., Snieckus V., and Eltis L.D. Purification and preliminary characterization of a serine hydrolase involved in the microbial degradation of polychlorinated biphenyls. J. Biol. Chem. 273 (1998) 22943-22949
    • (1998) J. Biol. Chem. , vol.273 , pp. 22943-22949
    • Seah, S.Y.K.1    Terracina, G.2    Bolin, J.T.3    Riebel, P.4    Snieckus, V.5    Eltis, L.D.6
  • 15
    • 0034520920 scopus 로고    scopus 로고
    • Toluene degradation pathway from Pseudomonas putida F1: substrate specificity and gene induction by 1-substituted benzenes
    • Cho M.C., Kang D.O., Yoon B.D., and Lee K. Toluene degradation pathway from Pseudomonas putida F1: substrate specificity and gene induction by 1-substituted benzenes. J. Ind. Microbiol. Biotech. 25 (2000) 163-170
    • (2000) J. Ind. Microbiol. Biotech. , vol.25 , pp. 163-170
    • Cho, M.C.1    Kang, D.O.2    Yoon, B.D.3    Lee, K.4
  • 16
    • 0030776495 scopus 로고    scopus 로고
    • Purification, characterization, and stereochemical analysis of a C-C hydrolase: 2-hydroxy-6-keto-nona-2,4-diene-1,9-dioic acid 5,6-hydrolase
    • Lam W.W.Y., and Bugg T.D.H. Purification, characterization, and stereochemical analysis of a C-C hydrolase: 2-hydroxy-6-keto-nona-2,4-diene-1,9-dioic acid 5,6-hydrolase. Biochemistry 36 (1997) 12242-12251
    • (1997) Biochemistry , vol.36 , pp. 12242-12251
    • Lam, W.W.Y.1    Bugg, T.D.H.2
  • 17
    • 0030870888 scopus 로고    scopus 로고
    • Pre-steady-state kinetic analysis of 2-hydroxy-6-keto-nona-2,4-diene-1,9-dioic acid 5,6-hydrolase: kinetic evidence for enol/keto tautomerization
    • Henderson I.M.J., and Bugg T.D.H. Pre-steady-state kinetic analysis of 2-hydroxy-6-keto-nona-2,4-diene-1,9-dioic acid 5,6-hydrolase: kinetic evidence for enol/keto tautomerization. Biochemistry 36 (1997) 12252-12258
    • (1997) Biochemistry , vol.36 , pp. 12252-12258
    • Henderson, I.M.J.1    Bugg, T.D.H.2
  • 18
    • 0034673180 scopus 로고    scopus 로고
    • Catalytic mechanism of a C-C hydrolase enzyme: evidence for a gem-diol intermediate, not an acyl enzyme
    • Fleming S.M., Robertson T.A., Langley G.J., and Bugg T.D.H. Catalytic mechanism of a C-C hydrolase enzyme: evidence for a gem-diol intermediate, not an acyl enzyme. Biochemistry 39 (2000) 1522-1531
    • (2000) Biochemistry , vol.39 , pp. 1522-1531
    • Fleming, S.M.1    Robertson, T.A.2    Langley, G.J.3    Bugg, T.D.H.4
  • 20
    • 12344275671 scopus 로고    scopus 로고
    • Catalytic mechanism of C-C hydrolase MhpC from Escherichia coli: kinetic analysis of His263 and Ser110 site-directed mutants
    • Li C., Montgomery M.G., Mohammed F., Li J.J., Wood S.P., and Bugg T.D. Catalytic mechanism of C-C hydrolase MhpC from Escherichia coli: kinetic analysis of His263 and Ser110 site-directed mutants. J. Mol. Biol. 346 (2005) 241-251
    • (2005) J. Mol. Biol. , vol.346 , pp. 241-251
    • Li, C.1    Montgomery, M.G.2    Mohammed, F.3    Li, J.J.4    Wood, S.P.5    Bugg, T.D.6
  • 21
    • 0028943123 scopus 로고
    • Identification of functional residues in a 2-hydroxymuconic semialdehyde hydrolase. A new member of the alpha/beta hydrolase-fold family of enzymes which cleaves carbon-carbon bonds
    • Diaz E., and Timmis K.N. Identification of functional residues in a 2-hydroxymuconic semialdehyde hydrolase. A new member of the alpha/beta hydrolase-fold family of enzymes which cleaves carbon-carbon bonds. J. Biol. Chem. 270 (1995) 6403-6411
    • (1995) J. Biol. Chem. , vol.270 , pp. 6403-6411
    • Diaz, E.1    Timmis, K.N.2
  • 22
    • 0030000545 scopus 로고    scopus 로고
    • Cloning, nucleotide sequence, and characterization of the genes encoding enzymes involved in the degradation of cumene to 2-hydroxy-6-oxo-7-methylocta-2,4-dienoic acid in Pseudomonas fluorescens IP01
    • Aoki H., Kimura T., Habe H., Yamane H., Kodama T., and Omori T. Cloning, nucleotide sequence, and characterization of the genes encoding enzymes involved in the degradation of cumene to 2-hydroxy-6-oxo-7-methylocta-2,4-dienoic acid in Pseudomonas fluorescens IP01. J. Ferment. Bioeng. 81 (1996) 187-196
    • (1996) J. Ferment. Bioeng. , vol.81 , pp. 187-196
    • Aoki, H.1    Kimura, T.2    Habe, H.3    Yamane, H.4    Kodama, T.5    Omori, T.6
  • 23
    • 0029996226 scopus 로고    scopus 로고
    • Cloning and nucleotide sequences of the genes involved in the meta-cleavage pathway of cumene degradation in Pseudomonas fluorescens IP01
    • Habe H., Kimura T., Nojiri H., Yamane H., and Omori T. Cloning and nucleotide sequences of the genes involved in the meta-cleavage pathway of cumene degradation in Pseudomonas fluorescens IP01. J. Ferment. Bioeng. 81 (1996) 247-254
    • (1996) J. Ferment. Bioeng. , vol.81 , pp. 247-254
    • Habe, H.1    Kimura, T.2    Nojiri, H.3    Yamane, H.4    Omori, T.5
  • 24
    • 0030000836 scopus 로고    scopus 로고
    • Analysis of cumene (isopropylbenzene) degradation genes from Pseudomonas fluorescens IP01
    • Habe H., Kasuga K., Nojiri H., Yamane H., and Omori T. Analysis of cumene (isopropylbenzene) degradation genes from Pseudomonas fluorescens IP01. Appl. Environ. Microbiol. 62 (1996) 4471-4477
    • (1996) Appl. Environ. Microbiol. , vol.62 , pp. 4471-4477
    • Habe, H.1    Kasuga, K.2    Nojiri, H.3    Yamane, H.4    Omori, T.5
  • 25
    • 0036308433 scopus 로고    scopus 로고
    • Purification, characterization, and steady-state kinetics of a meta-cleavage compound hydrolase from Pseudomonas fluorescens IP01
    • Saku T., Fushinobu S., Jun S.Y., Ikeda N., Nojiri H., Yamane H., Omori T., and Wakagi T. Purification, characterization, and steady-state kinetics of a meta-cleavage compound hydrolase from Pseudomonas fluorescens IP01. J. Biosci. Bioeng. 93 (2002) 567-574
    • (2002) J. Biosci. Bioeng. , vol.93 , pp. 567-574
    • Saku, T.1    Fushinobu, S.2    Jun, S.Y.3    Ikeda, N.4    Nojiri, H.5    Yamane, H.6    Omori, T.7    Wakagi, T.8
  • 27
    • 0025737846 scopus 로고
    • Location and sequence of the todF gene encoding 2-hydroxy-6-oxohepta-2,4-dienoate hydrolase in Pseudomonas putida F1
    • Menn F.M., Zylstra G.J., and Gibson D.T. Location and sequence of the todF gene encoding 2-hydroxy-6-oxohepta-2,4-dienoate hydrolase in Pseudomonas putida F1. Gene 104 (1991) 91-94
    • (1991) Gene , vol.104 , pp. 91-94
    • Menn, F.M.1    Zylstra, G.J.2    Gibson, D.T.3
  • 28
    • 0026095338 scopus 로고
    • DNA sequence determination of the TOL plasmid (pWWO) xylGFJ genes of Pseudomonas putida: implications for the evolution of aromatic catabolism
    • Horn J.M., Harayama S., and Timmis K.N. DNA sequence determination of the TOL plasmid (pWWO) xylGFJ genes of Pseudomonas putida: implications for the evolution of aromatic catabolism. Mol. Microbiol. 5 (1991) 2459-2474
    • (1991) Mol. Microbiol. , vol.5 , pp. 2459-2474
    • Horn, J.M.1    Harayama, S.2    Timmis, K.N.3
  • 30
    • 0036708001 scopus 로고    scopus 로고
    • Crystal structures of a meta-cleavage product hydrolase from Pseudomonas fluorescens IP01 (CumD) complexed with cleavage products
    • Fushinobu S., Saku T., Hidaka M., Jun S.Y., Nojiri H., Yamane H., Shoun H., Omori T., and Wakagi T. Crystal structures of a meta-cleavage product hydrolase from Pseudomonas fluorescens IP01 (CumD) complexed with cleavage products. Protein Sci. 11 (2002) 2184-2195
    • (2002) Protein Sci. , vol.11 , pp. 2184-2195
    • Fushinobu, S.1    Saku, T.2    Hidaka, M.3    Jun, S.Y.4    Nojiri, H.5    Yamane, H.6    Shoun, H.7    Omori, T.8    Wakagi, T.9
  • 31
    • 17844366884 scopus 로고    scopus 로고
    • A series of crystal structures of a meta-cleavage product hydrolase from Pseudomonas fluorescens IP01 (CumD) complexed with various cleavage products
    • Fushinobu S., Jun S.Y., Hidaka M., Nojiri H., Yamane H., Shoun H., Omori T., and Wakagi T. A series of crystal structures of a meta-cleavage product hydrolase from Pseudomonas fluorescens IP01 (CumD) complexed with various cleavage products. Biosci. Biotechnol. Biochem. 69 (2005) 491-498
    • (2005) Biosci. Biotechnol. Biochem. , vol.69 , pp. 491-498
    • Fushinobu, S.1    Jun, S.Y.2    Hidaka, M.3    Nojiri, H.4    Yamane, H.5    Shoun, H.6    Omori, T.7    Wakagi, T.8
  • 32
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276 (1997) 307-326
    • (1997) Methods Enzymol. , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 33
    • 0032790081 scopus 로고    scopus 로고
    • XtalView/Xfit - a versatile program for manipulating atomic coordinates and electron density
    • McRee D.E. XtalView/Xfit - a versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125 (1999) 156-165
    • (1999) J. Struct. Biol. , vol.125 , pp. 156-165
    • McRee, D.E.1
  • 34
    • 0000097225 scopus 로고    scopus 로고
    • SPOCK: Real-time collaborative molecular modeling
    • Christopher J.A., and Baldwin T.O. SPOCK: Real-time collaborative molecular modeling. J. Mol. Graph. Model. 16 (1998) 285
    • (1998) J. Mol. Graph. Model. , vol.16 , pp. 285
    • Christopher, J.A.1    Baldwin, T.O.2
  • 35
    • 0030815133 scopus 로고    scopus 로고
    • Raster3D: photorealistic molecular graphics
    • Merritt E.A., and Bacon D.J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277 (1997) 505-524
    • (1997) Methods Enzymol. , vol.277 , pp. 505-524
    • Merritt, E.A.1    Bacon, D.J.2
  • 36
    • 0026244229 scopus 로고
    • MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures
    • Kraulis P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24 (1991) 946-950
    • (1991) J. Appl. Crystallogr. , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 37
    • 0035933281 scopus 로고    scopus 로고
    • Crystal structure of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HPDA) hydrolase (BphD enzyme) from the Rhodococcus sp. strain RHA1 of the PCB degradation pathway
    • Nandhagopal N., Yamada A., Hatta T., Masai E., Fukuda M., Mitsui Y., and Senda T. Crystal structure of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HPDA) hydrolase (BphD enzyme) from the Rhodococcus sp. strain RHA1 of the PCB degradation pathway. J. Mol. Biol. 309 (2001) 1139-1151
    • (2001) J. Mol. Biol. , vol.309 , pp. 1139-1151
    • Nandhagopal, N.1    Yamada, A.2    Hatta, T.3    Masai, E.4    Fukuda, M.5    Mitsui, Y.6    Senda, T.7
  • 40
    • 0026681635 scopus 로고
    • Quantitative interpretations of double mutations of enzymes
    • Mildvan A.S., Weber D.J., and Kuliopulos A. Quantitative interpretations of double mutations of enzymes. Arch. Biochem. Biophys. 294 (1992) 327-340
    • (1992) Arch. Biochem. Biophys. , vol.294 , pp. 327-340
    • Mildvan, A.S.1    Weber, D.J.2    Kuliopulos, A.3


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