Purification and partial characterization of the extradiol dioxygenase, 2′-carboxy-2,3-dihydroxybiphenyl 1,2-dioxygenase, in the fluorene degradation pathway from Rhodococcus sp. strain DFA3

References

• Harayama S, Rekik M. Bacterial aromatic ring-cleavage enzymes are classified into two different gene families. J. Biol. Chem. 1989;264:15328–15333.
   PubMed Web of Science ®Google Scholar
• Vaillancourt FH, Bolin JT, Eltis LD. The ins and outs of ring-cleaving dioxygenases. Crit. Rev. Biochem. Mol. Biol. 2006;41:241–267.10.1080/10409230600817422
   PubMed Web of Science ®Google Scholar
• Han S, Eltis LD, Timmis KN, et al. Crystal structure of the biphenyl-cleaving extradiol dioxygenase from a PCB-degrading pseudomonad. Science. 1995;270:976–980.10.1126/science.270.5238.976
   PubMed Web of Science ®Google Scholar
• Senda T, Sugiyama K, Narita H, et al. Three-dimensional structures of free form and two substrate complexes of an extradiol ring-cleavage type dioxygenase, the BphC enzyme from Pseudomonas sp. strain KKS102. J. Mol. Biol. 1996;255:735–752.10.1006/jmbi.1996.0060
   PubMed Web of Science ®Google Scholar
• Kita A, Kita S, Fujisawa I, et al. An archetypical extradiol-cleaving catecholic dioxygenase: the crystal structure of catechol 2,3-dioxygenase (metapyrocatechase) from Pseudomonas putida mt-2. Structure. 1999;7:25–34.10.1016/S0969-2126(99)80006-9
   PubMed Web of Science ®Google Scholar
• Sugimoto K, Senda T, Aoshima H, et al. Crystal structure of an aromatic ring opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, under aerobic conditions. Structure. 1999;7:953–965.10.1016/S0969-2126(99)80122-1
   PubMed Web of Science ®Google Scholar
• Adams MA, Singh VK, Keller BO, et al. Structural and biochemical characterization of gentisate 1,2-dioxygenase from Escherichia coli O157:H7. Mol. Microbiol. 2006;61:1469–1484.10.1111/mmi.2006.61.issue-6
   PubMed Web of Science ®Google Scholar
• Keith LH, Telliard WA. ES&T special report: priority pollutants: I-a perspective view. Environ. Sci. Technol. 1979;13:416–423.10.1021/es60152a601
   Web of Science ®Google Scholar
• Fortnagel P, Harms H, Wittich RM, et al. Cleavage of dibenzofuran and dibenzodioxin ring systems by a Pseudomonas bacterium. Naturwissenschaften. 1989;76:222–223.10.1007/BF00627694
   PubMed Web of Science ®Google Scholar
• Wittich RM, Wilkes H, Sinnwell V, et al. Metabolism of dibenzo-p-dioxin by Sphingomonas sp. strain RW1. Appl. Environ. Microbiol. 1992;58:1005–1010.
   PubMed Web of Science ®Google Scholar
• Habe H, Chung JS, Kato H, et al. Characterization of the upper pathway genes for fluorene metabolism in Terrabacter sp. strain DBF63. J. Bacteriol. 2004;186:5938–5944.10.1128/JB.186.17.5938-5944.2004
   PubMed Web of Science ®Google Scholar
• Monna L, Omori T, Kodama T. Microbial degradation of dibenzofuran, fluorene, and dibenzo-p-dioxin by Staphylococcus auriculans DBF63. Appl Environ Microbiol. 1993;59:285–289.
   PubMed Web of Science ®Google Scholar
• Noumura T, Habe H, Widada J, et al. Genetic characterization of the dibenzofuran-degrading Actinobacteria carrying the dbfA1A2 gene homologues isolated from activated sludge. FEMS Microbiol. Lett. 2004;239:147–155.10.1016/j.femsle.2004.08.032
   PubMed Web of Science ®Google Scholar
• Sambrook J, Russell D. Molecular cloning: a laboratory manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory; 2001.
   Google Scholar
• Bimboim HC, Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 1979;7:1513–1523.10.1093/nar/7.6.1513
   PubMed Web of Science ®Google Scholar
• Bradford MM. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 1976;72:248–254.10.1016/0003-2697(76)90527-3
   PubMed Web of Science ®Google Scholar
• Schägger H. Tricine-SDS-PAGE. Nat. Protoc. 2006;1:16–22.10.1038/nprot.2006.4
   PubMed Web of Science ®Google Scholar
• Happe B, Eltis LD, Poth H, et al. Characterization of 2,2′,3-trihydroxybiphenyl dioxygenase, an extradiol dioxygenase from the dibenzofuran- and dibenzo-p-dioxin-degrading bacterium Sphingomonas sp. strain RW1. J. Bacteriol. 1993;175:7313–7320.
   PubMed Web of Science ®Google Scholar
• Sugimoto K, Senda M, Kasai D, et al. Molecular mechanism of strict substrate specificity of an extradiol dioxygenase, DesB, derived from Sphingobium sp. SYK-6. PLoS ONE. 2014;9:e92249. doi:10.1371/journal.pone.0092249.
   Google Scholar
• Li dF, Zhang JY, Hou YJ, et al. Structures of aminophenol dioxygenase in complex with intermediate, product and inhibitor. Acta Crystallogr. D Biol. Crystallogr. 2013;69:32–43.10.1107/S0907444912042072
   PubMed Web of Science ®Google Scholar
• IWATA K, Nojiri H, Shimizu K, et al. Expression, purification, and characterization of 2′-aminobiphenyl-2,3-diol 1,2-dioxygenase from carbazole-degrader Pseudomonas resinovorans strain CA10. Biosci. Biotechnol. Biochem. 2003;67:300–307.10.1271/bbb.67.300
   PubMed Web of Science ®Google Scholar
• Oba S, Suzuki T, Maeda R, et al. Characterization and genetic analyses of a carbazole-degrading gram-positive marine isolate, Janibacter sp. strain OC11. Biosci. Biotechnol. Biochem. 2014;78:1094–1101.10.1080/09168451.2014.917260
   PubMed Web of Science ®Google Scholar
• Fielding AJ, Kovaleva EG, Farquhar ER, et al. A hyperactive cobalt-substituted extradiol-cleaving catechol dioxygenase. J. Biol. Inorg. Chem. 2011;16:341–355.10.1007/s00775-010-0732-0
   PubMed Web of Science ®Google Scholar
• Jackson TA, Brunold TC. Combined spectroscopic/computational studies on Fe- and Mn-dependent superoxide dismutases: insights into second-sphere tuning of active site properties. Acc. Chem. Res. 2004;37:461–470.10.1021/ar030272h
   PubMed Web of Science ®Google Scholar
• Park HS, Kim HS. Identification and characterization of the nitrobenzene catabolic plasmids pNB1 and pNB2 in Pseudomonas putida HS12. J. Bacteriol. 2000;182:573–580.10.1128/JB.182.3.573-580.2000
   PubMed Web of Science ®Google Scholar
• Takenaka S, Murakami S, Shinke R, et al. Novel genes encoding 2-aminophenol 1,6-dioxygenase from Pseudomonas species AP-3 growing on 2-aminophenol and catalytic properties of the purified enzyme. J. Biol. Chem. 1997;272:14727–14732.10.1074/jbc.272.23.14727
   PubMed Web of Science ®Google Scholar
• Wu JF, Sun CW, Jiang CY, et al. A novel 2-aminophenol 1,6-dioxygenase involved in the degradation of p-chloronitrobenzene by Comamonas strain CNB-1: purification, properties, genetic cloning and expression in Escherichia coli. Arch. Microbiol. 2005;183:1–8.10.1007/s00203-004-0738-5
   PubMed Web of Science ®Google Scholar
• Eaton RW. Plasmid-encoded phthalate catabolic pathway in Arthrobacter keyseri 12B. J. Bacteriol. 2001;183:3689–3703.10.1128/JB.183.12.3689-3703.2001
   PubMed Web of Science ®Google Scholar
• Kasai D, Masai E, Miyauchi K, et al. Characterization of the gallate dioxygenase gene: three distinct ring cleavage dioxygenases are involved in syringate degradation by Sphingomonas paucimobilis SYK-6. J. Bacteriol. 2005;187:5067–5074.10.1128/JB.187.15.5067-5074.2005
   PubMed Web of Science ®Google Scholar
• Laurie AD1, Lloyd-Jones G. The phn genes of Burkholderia sp. strain RP007 constitute a divergent gene cluster for polycyclic aromatic hydrocarbon catabolism. J. Bacteriol. 1999;181:531–540.
   PubMed Web of Science ®Google Scholar