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Original Articles

A Series of Crystal Structures of a meta-Cleavage Product Hydrolase from Pseudomonas fluorescens IP01 (CumD) Complexed with Various Cleavage Products

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Pages 491-498 | Received 27 Aug 2004, Accepted 02 Dec 2004, Published online: 22 May 2014

  • 1) Patnaik, P., Hydrocarbons, aromatic. In “A Comprehensive Guide to the Hazardous Properties of Chemical Substances”, Van Nostrand Reinhold, New York, pp. 425–445 (1992).
  • 2) Nojiri, H., Habe, H., and Omori, T., Bacterial degradation of aromatic compounds via angular dioxygenation. J. Gen. Appl. Microbiol., 47, 279–305 (2001).
  • 3) Nojiri, H., and Omori, T., Molecular bases of aerobic bacterial degradation of dioxins: Involvement of angular dioxygenation. Biosci. Biotechnol. Biochem., 66, 2001–2016 (2002).
  • 4) Habe, H., and Omori, T., Genetics of polycyclic aromatic hydrocarbon metabolism in diverse aerobic bacteria. Biosci. Biotechnol. Biochem., 67, 225–243 (2003).
  • 5) Dagley, S., Biochemistry of aromatic hydrocarbon degradation in Pseudomonads. In “The Bacteria” Vol. 10, eds. Sokatch, J. R., and Ornston, L. N., Academic Press, New York, pp. 527–555 (1986).
  • 6) 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, 22943–22949 (1998).
  • 7) Hernáez, M. J., Andujar, E., Rios, J. L., Kaschabek, S. R., Reineke, W., and Santero, E., Identification of a serine hydrolase which cleaves the alicyclic ring of tetralin. J. Bacteriol., 182, 5448–5453 (2000).
  • 8) Furukawa, K., Tomizuka, N., and Kamibayashi, A., Effect of chlorine substitution on the bacterial metabolism of various polychlorinated biphenyls. Appl. Environ. Microbiol., 38, 301–310 (1979).
  • 9) 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, 5224–5232 (1993).
  • 10) Bedard, D. L., and Haberl, M. L., Influence of chlorine substitution pattern on the degradation of polychlorinated biphenyls by eight bacterial strains. Microbiol. Ecol., 20, 87–102 (1990).
  • 11) 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, 2654–2658 (1995).
  • 12) 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. Indust. Microbiol. Biotechnol., 25, 163–170 (2000).
  • 13) 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, 15701–15708 (2000).
  • 14) 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, 1511–1516 (2001).
  • 15) 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, 187–196 (1996).
  • 16) 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, 247–254 (1996).
  • 17) 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, 4471–4477 (1996).
  • 18) 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, 567–574 (2002).
  • 19) 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, 1139–1151 (2001).
  • 20) 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, 2184–2195 (2002).
  • 21) Habe, H., Morii, K., Fushinobu, S., Nam, J. W., Ayabe, Y., Yoshida, T., Wakagi, T., Yamane, H., Nojiri, H., and Omori, T., Crystal structure of a histidine-tagged serine hydrolase involved in the carbazole degradation (CarC enzyme). Biochem. Biophys. Res. Commun., 303, 631–639 (2003).
  • 22) Nardini, M., and Dijkstra, B. W., α/β hydrolase fold enzymes: The family keeps growing. Curr. Opin. Struct. Biol., 9, 732–737 (1999).
  • 23) Steller, I., Bolotovsky, R., and Rossmann, M. G., An algorithm for automatic indexing of oscillation images using Fourier analysis. J. Appl. Cryst., 30, 1036–1040 (1997).
  • 24) Powell, H. R., The Rossmann Fourier autoindexing algorithm in MOSFLM. Acta Cryst., D55, 1690–1695 (1999).
  • 25) Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L., Crystallography and NMR system: A new software suite for macromolecular structure determination. Acta Cryst., D54, 905–921 (1998).
  • 26) McRee, D. E., XtalView/Xfit — a versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol., 125, 156–165 (1999).
  • 27) Kraulis, P. J., MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst., 24, 946–950 (1991).
  • 28) Merritt, E. A., and Bacon, D. J., Raster3D: Photorealistic molecular graphics. Methods Enzymol., 277, 505–524 (1997).
  • 29) 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, 6403–6411 (1995).
  • 30) Pokorny, D., Steiner, W., and Ribbons, D. W., β-Ketolases — forgotten hydrolytic enzymes? Trends Biotechnol., 15, 291–296 (1997).
  • 31) 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, 12252–12258 (1997).
  • 32) 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, 1522–1531 (2000).
  • 33) Bugg, T. D., Fleming, S. M., Robertson, T. A., and Langley, G. J., 2-Hydroxy-6-keto-nona-2,4-diene 1,9-dioic acid 5,6-hydrolase: Evidence from 18O isotope exchange for gem-diol intermediate. Methods Enzymol., 354, 106–118 (2002).
  • 34) Nojiri, H., Taira, H., Iwata, K., Morii, K., Nam, J. W., Yoshida, T., Habe, H., Nakamura, S., Shimizu, K., Yamane, H., and Omori, T., Purification and characterization of meta-cleavage compound hydrolase from a carbazole degrader Pseudomonas resinovorans strain CA10. Biosci. Biotechnol. Biochem., 67, 36–45 (2003).

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