Advanced search
Publication Cover
Bioscience, Biotechnology, and Biochemistry Volume 72, 2008 - Issue 12
Journal homepage
277
Views
8
CrossRef citations to date
0
Altmetric
Original Articles

Alteration of the Substrate Specificity of the Angular Dioxygenase Carbazole 1,9a-Dioxygenase

Hiromasa UCHIMURABiotechnology Research Center, The University of Tokyo
,
Tadafumi HORISAKIBiotechnology Research Center, The University of Tokyo;Department of Chemistry, Faculty of Science, Tokyo University of Science
,
Takashi UMEDABiotechnology Research Center, The University of Tokyo
,
Haruko NOGUCHIBiotechnology Research Center, The University of Tokyo;Professional Program for Agricultural Bioinformatics, The University of Tokyo
,
Yusuke USAMIBiotechnology Research Center, The University of Tokyo
,
Li LIBiotechnology Research Center, The University of Tokyo
,
Tohru TERADAProfessional Program for Agricultural Bioinformatics, The University of Tokyo
,
Shugo NAKAMURADepartment of Biotechnology, The University of Tokyo
,
Kentaro SHIMIZUProfessional Program for Agricultural Bioinformatics, The University of Tokyo;Department of Biotechnology, The University of Tokyo
,
Tetsuo TAKEMURADepartment of Chemistry, Faculty of Science, Tokyo University of Science
,
Hiroshi HABEBiotechnology Research Center, The University of Tokyo
,
Kazuo FURIHATADepartment of Applied Biological Chemistry, The University of Tokyo
,
Toshio OMORIBiotechnology Research Center, The University of Tokyo
,
Hisakazu YAMANEBiotechnology Research Center, The University of Tokyo
&
Hideaki NOJIRIBiotechnology Research Center, The University of Tokyo;Professional Program for Agricultural Bioinformatics, The University of Tokyo
 show all
Pages 3237-3248 | Received 28 Jul 2008, Accepted 27 Aug 2008, Published online: 22 May 2014

  • 1) Boyd, D. R., and Sheldrake, G. N., The dioxygenase-catalyzed formation of vicinal cis-diols. Nat. Prod. Rep., 15, 309–325 (1998).
  • 2) Parales, R. E., and Resnick, S. M., Aromatic ring hydroxylating dioxygenases. In “Pseudomonas Volume 4,” eds. Ramos, J.-L., and Levesque, R. C., Springer, New York, pp. 287–340 (2006).
  • 3) Arcos, J. C., and Argus, M. F., Molecular geometry and carcinogenic activity of aromatic compounds. New perspectives. Adv. Cancer Res., 11, 305–471 (1968).
  • 4) Nojiri, H., and Omori, T., Carbazole metabolism by pseudomonads. In “Pseudomonas Volume 5,” eds. Ramos, J.-L., and Filloux, A., Springer, New York, pp. 107–145 (2007).
  • 5) Sato, S., Nam, J.-W., Kasuga, K., Nojiri, H., Yamane, H., and Omori, T., Identification and characterization of genes encoding carbazole 1,9a-dioxygenase in Pseudomonas sp. strain CA10. J. Bacteriol., 179, 4850–4858 (1997).
  • 6) Nojiri, H., Nam, J.-W., Kosaka, M., Morii, K., Takemura, T., Furihata, K., Yamane, H., and Omori, T., Diverse oxygenation catalyzed by carbazole 1,9a-dioxygenase from Pseudomonas sp. strain CA10. J. Bacteriol., 181, 3105–3113 (1999).
  • 7) Nojiri, H., and Omori, T., Molecular bases of aerobic bacterial degradation of dioxins: involvement of angular dioxygenation. Biosci. Biotechnol. Biochem., 66, 2001–2016 (2002).
  • 8) Nam, J.-W., Nojiri, H., Noguchi, H., Uchimura, H., Yoshida, T., Habe, H., Yamane, H., and Omori, T., Purification and characterization of carbazole 1,9a-dioxygenase, a three-component dioxygenase system of Pseudomonas resinovorans strain CA10. Appl. Environ. Microbiol., 68, 5882–5890 (2002).
  • 9) Takagi, T., Nojiri, H., Yoshida, T., Habe, H., and Omori, T., Detailed comparison between the substrate specificities of two angular dioxygenases, dibenzofuran 4,4a-dioxygenase from Terrabacter sp. and carbazole 1,9a-dioxygenase from Pseudomonas resinovorans. Biotechnol. Lett., 24, 2099–2106 (2002).
  • 10) Nojiri, H., Ashikawa, Y., Noguchi, H., Nam, J.-W., Urata, M., Fujimoto, Z., Uchimura, H., Terada, T., Nakamura, S., Shimizu, K., Yoshida, T., Habe, H., and Omori, T., Structure of the terminal oxygenase component of angular dioxygenase, carbazole 1,9a-dioxygenase. J. Mol. Biol., 351, 355–370 (2005).
  • 11) Ashikawa, Y., Fujimoto, Z., Noguchi, H., Habe, H., Omori, T., Yamane, H., and Nojiri, H., Electron transfer complex formation between oxygenase and ferredoxin components in Rieske nonheme iron oxygenase system. Structure, 14, 1779–1789 (2006).
  • 12) Sambrook, J., and Russell, D. W., “Molecular Cloning, a Laboratory Manual” 3rd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor (2001).
  • 13) Nojiri, H., Sekiguchi, H., Maeda, K., Urata, M., Nakai, S., Yoshida, T., Habe, H., and Omori, T., Genetic characterization and evolutionary implications of car gene cluster in the carbazole degrader Pseudomonas sp. strain CA10. J. Bacteriol., 183, 3663–3679 (2001).
  • 14) DeLano, W. L., “The PyMOL User’s Manual,” DeLano Scientific, San Carlos (2001).
  • 15) Inoue, K., Widada, J., Nakai, S., Endoh, T., Urata, M., Ashikawa, Y., Shintani, M., Saiki, Y., Yoshida, T., Habe, H., Omori, T., and Nojiri, H., Divergent structures of carbazole degradative car operon isolated from Gram-negative bacteria. Biosci. Biotechnol. Biochem., 68, 1467–1480 (2004).
  • 16) Grifoll, M., Selifonov, S. A., Gatlin, C. V., and Chapman, P. J., Actions of a versatile fluorene-degrading bacterial isolate on polycyclic aromatic compounds. Appl. Environ. Microbiol., 61, 3711–3723 (1995).
  • 17) Kasuga, K., Habe, H., Chung, J.-S., Yoshida, T., Nojiri, H., Yamane, H., and Omori, T., Isolation and characterization of the genes encoding a novel oxygenase component of angular dioxygenase from Gram-positive dibenzofuran-degrader Terrabacter sp. strain DBF63. Biochem. Biophys. Res. Commun., 283, 195–204 (2001).
  • 18) Bradford, M. M., A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein dye binding. Anal. Biochem., 72, 248–254 (1976).
  • 19) Ferraro, D. J., Brown, E. N., Yu, C.-L., Parales, R. E., Gibson, D. T., and Ramaswamy, S., Structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from Sphingomonas yanoikuyae B1. BMC Struct. Biol., 7, 10 (2007).
  • 20) Jakoncic, J., Jouanneau, Y., Meyer, C., and Stojanoff, V., The catalytic pocket of the ring-hydroxylating dioxygenase from Sphingomonas CHY-1. Biochem. Biophys. Res. Commun., 352, 861–866 (2007).
  • 21) Hegg, E. L., and Que, L., Jr., The 2-His-1-carboxylate facial triad: an emerging structural motif in mononuclear non-heme iron(II) enzymes. Eur. J. Biochem., 250, 625–629 (1997).
  • 22) Parales, R. E., Lee, K., Resnick, S. M., Jiang, H., Lessner, D. J., and Gibson, D. T., Substrate specificity of naphthalene dioxygenase: effect of specific amino acids at the active site of the enzyme. J. Bacteriol., 182, 1641–1649 (2000).
  • 23) Kauppi, B., Lee, K., Carredano, E., Parales, R. E., Gibson, D. T., Eklund, H., and Ramaswamy, S., Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2-dioxygenase. Structure, 6, 571–586 (1998).
  • 24) Parales, R. E., Resnick, S. M., Yu, C.-L., Boyd, D. R., Sharma, N. D., and Gibson, D. T., Regioselectivity and enantioselectivity of naphthalene dioxygenase during arene cis-dihydroxylation: control by phenylalanine 352 in the alpha subunit. J. Bacteriol., 182, 5495–5504 (2000).
  • 25) Lee, K.-S., Parales, J. V., Friemann, R., and Parales, R. E., Active site residues controlling substrate specificity in 2-nitrotoluene dioxygenase from Acidovorax sp. strain JS42. J. Ind. Microbiol. Biotechnol., 32, 465–473 (2005).
  • 26) Friemann, R., Ivkovic-Jensen, M. M., Lessner, D. J., Yu, C.-L., Gibson, D. T., Parales, R. E., Eklund, H., and Ramaswamy, S., Structural insight into the dioxygenation of nitroarene compounds: the crystal structure of nitrobenzene dioxygenase. J. Mol. Biol., 348, 1139–1151 (2005).
  • 27) Ju, K.-S., and Parales, R. E., Control of substrate specificity by active-site residues in nitrobenzene dioxygenase. Appl. Environ. Microbiol., 72, 1817–1824 (2006).
  • 28) Suenaga, H., Goto, M., and Furukawa, K., Emergence of multifunctional oxygenase activities by random priming recombination. J. Biol. Chem., 276, 22500–22506 (2001).
  • 29) Suenaga, H., Mitsuoka, M., Ura, Y., Watanabe, T., and Furukawa, K., Directed evolution of biphenyl dioxygenase: emergence of enhanced degradation capacity for benzene, toluene, and alkylbenzenes. J. Bacteriol., 183, 5441–5444 (2001).
  • 30) Suenaga, H., Watanabe, T., Sato, M., Ngadiman, and Furukawa, K., Alteration of regiospecificity in biphenyl dioxygenase by active-site engineering. J. Bacteriol., 184, 3682–3688 (2002).
  • 31) Furusawa, Y., Nagarajan, V., Tanokura, M., Masai, E., Fukuda, M., and Senda, T., Crystal structure of the terminal oxygenase component of biphenyl dioxygenase derived from Rhodococcus sp. strain RHA1. J. Mol. Biol., 342, 1041–1052 (2004).
  • 32) Ferraro, D. J., Gakhar, L., and Ramaswamy, S., Rieske business: structure-function of Rieske non-heme oxygenases. Biochem. Biophys. Res. Commun., 338, 175–190 (2005).
  • 33) Ferraro, D. J., Okerlund, A. L., Mowers, J. C., and Ramaswamy, S., Structural basis for regioselectivity and stereoselectivity of product formation by naphthalene 1,2-dioxygenase. J. Bacteriol., 188, 6986–6994 (2006).

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Order Reprints Request Corporate Permissions

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

Request Academic Permissions

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.

Related research

People also read lists articles that other readers of this article have read.

Recommended articles lists articles that we recommend and is powered by our AI driven recommendation engine.

Cited by lists all citing articles based on Crossref citations.
Articles with the Crossref icon will open in a new tab.