Evolutionary relationships among extradiol dioxygenases

This Article

	Full Text (PDF)
	Alert me when this article is cited
	Alert me if a correction is posted

Services

	Similar articles in this journal
	Similar articles in PubMed
	Alert me to new issues of the journal
	Download to citation manager
	Copyright Information
	Books from ASM Press
	MicrobeWorld

Citing Articles

	Citing Articles via HighWire
	Citing Articles via Google Scholar

Google Scholar

	Articles by Eltis, L. D.
	Articles by Bolin, J. T.
	Search for Related Content

PubMed

	PubMed Citation
	Articles by Eltis, L. D.
	Articles by Bolin, J. T.

J. Bacteriol., Oct 1996, 5930-5937, Vol 178, No. 20
Copyright © 1996, American Society for Microbiology

Evolutionary relationships among extradiol dioxygenases

LD Eltis and JT Bolin
Department of Biochemistry, Universite Laval, Quebec City, Canada. leltis@rsvs.ulaval.ca

A structure-validated alignment of 35 extradiol dioxygenase sequences including two-domain and one-domain enzymes was derived. Strictly conserved residues include the metal ion ligands and several catalytically essential active site residues, as well as a number of structurally important residues that are remote from the active site. Phylogenetic analyses based on this alignment indicate that the ancestral extradiol dioxygenase was a one-domain enzyme and that the two-domain enzymes arose from a single genetic duplication event. Subsequent divergence among the two-domain dioxygenases has resulted in several families, two of which are based on substrate preference. In several cases, the two domains of a given enzyme express different phylogenies, suggesting the possibility that such enzymes arose from the recombination of genes encoding different dioxygenases. A phylogeny- based classification system for extradiol dioxygenases is proposed.

This article has been cited by other articles:

Witzig, R., Junca, H., Hecht, H.-J., Pieper, D. H. (2006). Assessment of Toluene/Biphenyl Dioxygenase Gene Diversity in Benzene-Polluted Soils: Links between Benzene Biodegradation and Genes Similar to Those Encoding Isopropylbenzene Dioxygenases.. Appl. Environ. Microbiol. 72: 3504-3514 [Abstract] [Full Text]
Kasai, D., Masai, E., Miyauchi, K., Katayama, Y., Fukuda, M. (2005). Characterization of the Gallate Dioxygenase Gene: Three Distinct Ring Cleavage Dioxygenases Are Involved in Syringate Degradation by Sphingomonas paucimobilis SYK-6. J. Bacteriol. 187: 5067-5074 [Abstract] [Full Text]
Fortin, P. D., Lo, A. T.-F., Haro, M.-A., Kaschabek, S. R., Reineke, W., Eltis, L. D. (2005). Evolutionarily Divergent Extradiol Dioxygenases Possess Higher Specificities for Polychlorinated Biphenyl Metabolites. J. Bacteriol. 187: 415-421 [Abstract] [Full Text]
Junca, H., Plumeier, I., Hecht, H.-J., Pieper, D. H. (2004). Difference in kinetic behaviour of catechol 2,3-dioxygenase variants from a polluted environment. Microbiology 150: 4181-4187 [Abstract] [Full Text]
Viggiani, A., Siani, L., Notomista, E., Birolo, L., Pucci, P., Di Donato, A. (2004). The Role of the Conserved Residues His-246, His-199, and Tyr-255 in the Catalysis of Catechol 2,3-Dioxygenase from Pseudomonas stutzeri OX1. J. Biol. Chem. 279: 48630-48639 [Abstract] [Full Text]
Habe, H., Chung, J.-S., Kato, H., Ayabe, Y., Kasuga, K., Yoshida, T., Nojiri, H., Yamane, H., Omori, T. (2004). Characterization of the Upper Pathway Genes for Fluorene Metabolism in Terrabacter sp. Strain DBF63. J. Bacteriol. 186: 5938-5944 [Abstract] [Full Text]
Kasai, D., Masai, E., Miyauchi, K., Katayama, Y., Fukuda, M. (2004). Characterization of the 3-O-Methylgallate Dioxygenase Gene and Evidence of Multiple 3-O-Methylgallate Catabolic Pathways in Sphingomonas paucimobilis SYK-6. J. Bacteriol. 186: 4951-4959 [Abstract] [Full Text]
Ishida, T., Tanaka, H., Horiike, K. (2004). Quantitative Structure-Activity Relationship for the Cleavage of C3/C4-Substituted Catechols by a Prototypal Extradiol Catechol Dioxygenase with Broad Substrate Specificity. J Biochem 135: 721-730 [Abstract] [Full Text]
Vetting, M. W., Wackett, L. P., Que, L. Jr., Lipscomb, J. D., Ohlendorf, D. H. (2004). Crystallographic Comparison of Manganese- and Iron-Dependent Homoprotocatechuate 2,3-Dioxygenases. J. Bacteriol. 186: 1945-1958 [Abstract] [Full Text]
Miyazawa, D., Mukerjee-Dhar, G., Shimura, M., Hatta, T., Kimbara, K. (2004). Genes for Mn(II)-dependent NahC and Fe(II)-dependent NahH located in close proximity in the thermophilic naphthalene and PCB degrader, Bacillus sp. JF8: cloning and characterization. Microbiology 150: 993-1004 [Abstract] [Full Text]
Okuta, A., Ohnishi, K., Harayama, S. (2004). Construction of Chimeric Catechol 2,3-Dioxygenase Exhibiting Improved Activity against the Suicide Inhibitor 4-Methylcatechol. Appl. Environ. Microbiol. 70: 1804-1810 [Abstract] [Full Text]
Kasai, Y., Shindo, K., Harayama, S., Misawa, N. (2003). Molecular Characterization and Substrate Preference of a Polycyclic Aromatic Hydrocarbon Dioxygenase from Cycloclasticus sp. Strain A5. Appl. Environ. Microbiol. 69: 6688-6697 [Abstract] [Full Text]
Jeong, J. J., Kim, J. H., Kim, C.-K., Hwang, I., Lee, K. (2003). 3- and 4-alkylphenol degradation pathway in Pseudomonas sp. strain KL28: genetic organization of the lap gene cluster and substrate specificities of phenol hydroxylase and catechol 2,3-dioxygenase. Microbiology 149: 3265-3277 [Abstract] [Full Text]
Hatta, T., Mukerjee-Dhar, G., Damborsky, J., Kiyohara, H., Kimbara, K. (2003). Characterization of a Novel Thermostable Mn(II)-dependent 2,3-Dihydroxybiphenyl 1,2-Dioxygenase from a Polychlorinated Biphenyl- and Naphthalene-degrading Bacillus sp. JF8. J. Biol. Chem. 278: 21483-21492 [Abstract] [Full Text]
Andujar, E., Santero, E. (2003). Site-directed mutagenesis of an extradiol dioxygenase involved in tetralin biodegradation identifies residues important for activity or substrate specificity. Microbiology 149: 1559-1567 [Abstract] [Full Text]
McKay, D. B., Prucha, M., Reineke, W., Timmis, K. N., Pieper, D. H. (2003). Substrate Specificity and Expression of Three 2,3-Dihydroxybiphenyl 1,2-Dioxygenases from Rhodococcus globerulus Strain P6. J. Bacteriol. 185: 2944-2951 [Abstract] [Full Text]
Alfreider, A., Vogt, C., Babel, W. (2003). Expression of Chlorocatechol 1,2-Dioxygenase and Chlorocatechol 2,3-Dioxygenase Genes in Chlorobenzene-Contaminated Subsurface Samples. Appl. Environ. Microbiol. 69: 1372-1376 [Abstract] [Full Text]
Muraki, T., Taki, M., Hasegawa, Y., Iwaki, H., Lau, P. C. K. (2003). Prokaryotic Homologs of the Eukaryotic 3-Hydroxyanthranilate 3,4-Dioxygenase and 2-Amino-3-Carboxymuconate-6-Semialdehyde Decarboxylase in the 2-Nitrobenzoate Degradation Pathway of Pseudomonas fluorescens Strain KU-7. Appl. Environ. Microbiol. 69: 1564-1572 [Abstract] [Full Text]
Vaillancourt, F. H., Haro, M.-A., Drouin, N. M., Karim, Z., Maaroufi, H., Eltis, L. D. (2003). Characterization of Extradiol Dioxygenases from a Polychlorinated Biphenyl-Degrading Strain That Possess Higher Specificities for Chlorinated Metabolites. J. Bacteriol. 185: 1253-1260 [Abstract] [Full Text]
Diaz, E., Ferrandez, A., Prieto, M. A., Garcia, J. L. (2001). Biodegradation of Aromatic Compounds by Escherichia coli. Microbiol. Mol. Biol. Rev. 65: 523-569 [Abstract] [Full Text]
Riegert, U., Bürger, S., Stolz, A. (2001). Altering Catalytic Properties of 3-Chlorocatechol-Oxidizing Extradiol Dioxygenase from Sphingomonas xenophaga BN6 by Random Mutagenesis. J. Bacteriol. 183: 2322-2330 [Abstract] [Full Text]
Hernáez, M. J., Andújar, E., Ríos, J. L., Kaschabek, S. R., Reineke, W., Santero, E. (2000). Identification of a Serine Hydrolase Which Cleaves the Alicyclic Ring of Tetralin. J. Bacteriol. 182: 5448-5453 [Abstract] [Full Text]
Martin, V. J. J., Mohn, W. W. (2000). Genetic Investigation of the Catabolic Pathway for Degradation of Abietane Diterpenoids by Pseudomonas abietaniphila BKME-9. J. Bacteriol. 182: 3784-3793 [Abstract] [Full Text]
Dunwell, J. M., Khuri, S., Gane, P. J. (2000). Microbial Relatives of the Seed Storage Proteins of Higher Plants: Conservation of Structure and Diversification of Function during Evolution of the Cupin Superfamily. Microbiol. Mol. Biol. Rev. 64: 153-179 [Abstract] [Full Text]
Mesarch, M. B., Nakatsu, C. H., Nies, L. (2000). Development of Catechol 2,3-Dioxygenase-Specific Primers for Monitoring Bioremediation by Competitive Quantitative PCR. Appl. Environ. Microbiol. 66: 678-683 [Abstract] [Full Text]
Andújar, E., Hernáez, M. J., Kaschabek, S. R., Reineke, W., Santero, E. (2000). Identification of an Extradiol Dioxygenase Involved in Tetralin Biodegradation: Gene Sequence Analysis and Purification and Characterization of the Gene Product. J. Bacteriol. 182: 789-795 [Abstract] [Full Text]
Miyauchi, K., Adachi, Y., Nagata, Y., Takagi, M. (1999). Cloning and Sequencing of a Novel meta-Cleavage Dioxygenase Gene Whose Product Is Involved in Degradation of gamma -Hexachlorocyclohexane in Sphingomonas paucimobilis. J. Bacteriol. 181: 6712-6719 [Abstract] [Full Text]
Arai, H., Yamamoto, T., Ohishi, T., Shimizu, T., Nakata, T., Kudo, T. (1999). Genetic organization and characteristics of the 3-(3-hydroxyphenyl)propionic acid degradation pathway of Comamonas testosteroni TA441. Microbiology 145: 2813-2820 [Abstract] [Full Text]
Riegert, U., Heiss, G., Kuhm, A. E., Müller, C., Contzen, M., Knackmuss, H.-J., Stolz, A. (1999). Catalytic Properties of the 3-Chlorocatechol-Oxidizing 2,3-Dihydroxybiphenyl 1,2-Dioxygenase from Sphingomonas sp. Strain BN6. J. Bacteriol. 181: 4812-4817 [Abstract] [Full Text]
Mars, A. E., Kingma, J., Kaschabek, S. R., Reineke, W., Janssen, D. B. (1999). Conversion of 3-Chlorocatechol by Various Catechol 2,3-Dioxygenases and Sequence Analysis of the Chlorocatechol Dioxygenase Region of Pseudomonas putida GJ31. J. Bacteriol. 181: 1309-1318 [Abstract] [Full Text]
Haigler, B. E., Johnson, G. R., Suen, W.-C., Spain, J. C. (1999). Biochemical and Genetic Evidence for meta-Ring Cleavage of 2,4,5-Trihydroxytoluene in Burkholderia sp. Strain DNT. J. Bacteriol. 181: 965-972 [Abstract] [Full Text]
Laurie, A. D., Lloyd-Jones, G. (1999). The phn Genes of Burkholderia sp. Strain RP007 Constitute a Divergent Gene Cluster for Polycyclic Aromatic Hydrocarbon Catabolism. J. Bacteriol. 181: 531-540 [Abstract] [Full Text]
Beil, S., Timmis, K. N., Pieper, D. H. (1999). Genetic and Biochemical Analyses of the tec Operon Suggest a Route for Evolution of Chlorobenzene Degradation Genes. J. Bacteriol. 181: 341-346 [Abstract] [Full Text]
Vaillancourt, F. H., Han, S., Fortin, P. D., Bolin, J. T., Eltis, L. D. (1998). Molecular Basis for the Stabilization and Inhibition of 2,3-Dihydroxybiphenyl 1,2-Dioxygenase by t-Butanol. J. Biol. Chem. 273: 34887-34895 [Abstract] [Full Text]
Werwath, J., Arfmann, H.-A., Pieper, D. H., Timmis, K. N., Wittich, R.-M. (1998). Biochemical and Genetic Characterization of a Gentisate 1,2-Dioxygenase from Sphingomonas sp. Strain RW5. J. Bacteriol. 180: 4171-4176 [Abstract] [Full Text]
Peng, X., Egashira, T., Hanashiro, K., Masai, E., Nishikawa, S., Katayama, Y., Kimbara, K., Fukuda, M. (1998). Cloning of a Sphingomonas paucimobilis SYK-6 Gene Encoding a Novel Oxygenase That Cleaves Lignin-Related Biphenyl and Characterization of the Enzyme. Appl. Environ. Microbiol. 64: 2520-2527 [Abstract] [Full Text]
Hugo, N., Armengaud, J., Gaillard, J., Timmis, K. N., Jouanneau, Y. (1998). A Novel [2Fe-2S] Ferredoxin from Pseudomonas putida mt2 Promotes the Reductive Reactivation of Catechol 2,3-Dioxygenase. J. Biol. Chem. 273: 9622-9629 [Abstract] [Full Text]
Vaillancourt, F. H., Labbe, G., Drouin, N. M., Fortin, P. D., Eltis, L. D. (2002). The Mechanism-based Inactivation of 2,3-Dihydroxybiphenyl 1,2-Dioxygenase by Catecholic Substrates. J. Biol. Chem. 277: 2019-2027 [Abstract] [Full Text]

Appl. Environ. Microbiol.	Infect. Immun.	Eukaryot. Cell
Mol. Cell. Biol.	J. Virol.	Microbiol. Mol. Biol. Rev.
	ALL ASM JOURNALS