Quantitative structure-activity relationship for the cleavage of C3/C4-substituted catechols by a prototypal extradiol catechol dioxygenase with broad substrate specificity

Journal of Biochemistry

Volumn 135, Issue 6, 2004, Pages 721-730

  Ishida, Tetsuo ^a   Tanaka, Hiroyuki ^a   Horiike, Kihachiro ^a  

^a SHIGA UNIVERSITY OF MEDICAL SCIENCE   (Japan)

Author keywords

Catechols; Dioxygenase; Non heme iron; Oxygen; pK a values of catechols; Substituent effects

Indexed keywords

2 HYDROXYMUCONATE SEMIALDEHYDE; 3 PHENYLCATECHOL; 4 TERT BUTYLCATECHOL; CATECHOL; CATECHOL 2,3 DIOXYGENASE; CATECHOL DERIVATIVE; IRON; MUCONALDEHYDE; OXYGEN; UNCLASSIFIED DRUG;

ANAEROBIC METABOLISM; ARTICLE; BIODEGRADATION; CONTROLLED STUDY; ENZYME ACTIVE SITE; ENZYME KINETICS; ENZYME SPECIFICITY; NONHUMAN; PH; PKA; PSEUDOMONAS PUTIDA; QUANTITATIVE STRUCTURE ACTIVITY RELATION; REACTION ANALYSIS; SPECTROPHOTOMETRY; TEMPERATURE;

BINDING SITES; CATECHOL 2,3-DIOXYGENASE; CATECHOLS; DIOXYGENASES; HYDROGEN-ION CONCENTRATION; MOLECULAR STRUCTURE; PROTEIN CONFORMATION; PSEUDOMONAS PUTIDA; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY;

NEGIBACTERIA; PSEUDOMONAS; PSEUDOMONAS PUTIDA;

EID: 3142594034     PISSN: 0021924X     EISSN: None     Source Type: Journal    
DOI: 10.1093/jb/mvh089     Document Type: Article

References (36)

1. Worsey, M.J. and Williams, P.A. (1975) Metabolism of toluene and xylenes by Pseudomonas putida (arvilla) mt-2: Evidence for a new function of the TOL plasmid. J. Bacteriol. 124, 7-13
2. Greated, A., Lambertsen, L., Williams, P.A., and Thomas, C.M. (2002) Complete sequence of the IncP-9 TOL plasmid pWW0 from Pseudomonas putida. Environ. Microbiol. 4, 856-871
3. Maeda, K., Nojiri, H., Shintani, M., Yoshida, T., Habe, H., and Omori, T. (2003) Complete nucleotide sequence of carbazole/dioxin-degrading plasmid pCAR1 in Pseudomonas resinovorans strain CA10 indicates its mosaicity and the presence of large catabolic transposon Tn4676. J. Mol. Biol. 326, 21-33
4. Que, L., Jr., Widom, J., and Crawford, R.L. (1981) 3,4- Dihydroxyphenylacetate 2,3-dioxygenase. A manganese(II) dioxygenase from Bacillus brevis. J. Biol. Chem. 256, 10941-10944
5. Boldt, Y.R., Sadowsky, M.J., Ellis, L.B., Que, L., Jr., and Wackett, L.P. (1995) A manganese-dependent dioxygenase from Arthrobacter globiformis CM-2 belongs to the major extradiol dioxygenase family. J. Bacteriol. 177, 1225-1232
6. Hatta, T., Murkerjee-Dhar, G., Damborsky, J., Kiyohara, H., and 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
7. Eltis, L.D. and Bolin, J.T. (1996) Evolutionary relationships among extradiol dioxygenases. J. Bacteriol. 178, 5930-5937
8. Spence, E.L., Kawamukai, M., Sanvoisin, J., Braven, H., and Bugg, T.D.H. (1996) Catechol dioxygenases from Escherichia coli (MhpB) and Alcaligenes eutrophus (MpcI): Sequence analysis and biochemical properties of a third family of extradiol dioxygenases. J. Bacteriol. 178, 5249-5256
9. Sugimoto, K., Senda, T., Aoshima, H., Masai, E., Fukuda, M., and Mitsui, Y. (1999) Crystal structure of an aromatic ring opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, under aerobic conditions. Structure 7, 953-965
10. Ramos, J.L., Wasserfallen, A., Rose, K., and Timmis, K.N. (1987) Redesigning metabolic routes: Manipulation of TOL plasmid pathway for catabolism of alkylbenzoates. Science 235, 593-596
11. Cerdan, P., Wasserfallen, A., Rekik, M., Timmis, K.N., and Harayama, S. (1994) Substrate specificity of catechol 2,3-dioxygenase encoded by TOL plasmid pWW0 of Pseudomonas putida and its relationship to cell growth. J. Bacteriol. 176, 6074-6081
12. Dai, S., Vaillancourt, F.H., Maaroufi, H., Drouin, N.M., Neau, D.B., Snieckus, V., Bolin, J.T., and Eltis, L.D. (2002) Identification and analysis of a bottleneck in PCB biodegradation. Nat. Struct. Biol. 9, 934-939
13. Que, L., Jr. and Ho, R.Y.N. (1996) Dioxygen activation by enzymes with mononuclear non-heme iron active sites. Chem. Rev. 96, 2607-2624
14. Bugg, T.D.H., Sanvoisin, J., and Spence, E.L. (1997) Exploring the catalytic mechanism of the extradiol catechol dioxygenases. Biochem. Soc. Trans 25, 81-85
15. Lange, S.J. and Que, L., Jr. (1998) Oxygen activating nonheme iron enzymes. Curr. Opin. Chem. Biol. 2, 159-172
16. 2 activation. Curr. Opin. Chem. Biol. 5, 550-555
17. Vaillancourt, F.H., Barbosa, C.J., Spiro, T.G., Bolin, J.T., Blades, M.W., Turner, R.F.B., and Eltis, L.D. (2002) Definitive evidence for monoanionic binding of 2,3-dihydroxybiphenyl to 2,3-dihydroxybiphenyl 1,2-dioxygenase from UV resonance Raman spectroscopy, UV/Vis absorption spectroscopy, and crystallography. J. Amer. Chem. Soc. 124, 2485-2496
18. Sato, N., Uragami, Y., Nishizaki, T., Takahashi, Y., Sazaki, G., Sugimoto, K., Nonaka, T., Masai, E., Fukuda, M., and Senda, T. (2002) Crystal structures of the reaction intermediate and its homologue of an extradiol-cleaving catecholic dioxygenase. J. Mol. Biol. 321, 621-636
19. Spence, E.L., Langley, G.J., and Bugg, T.D.H. (1996) Cis-trans isomerization of a cyclopropyl radical trap catalyzed by extradiol catechol dioxygenases: Evidence for a semiquinone intermediate. J. Amer. Chem. Soc. 118, 8336-8343
20. Winfield, C.J., Al-Mahrizy, Z., Gravestock, M., and Bugg, T.D.H. (2000) Elucidation of the catalytic mechanisms of the non-heme iron-dependent catechol dioxygenases: Synthesis of carba analogues for hydroperoxide reaction intermediates. J. Chem. Soc. Perkin Trans. 1, 3277-3289
21. Sanvoisin, J., Langley, G.J., and Bugg, T.D.H. (1995) Mechanism of extradiol catechol dioxygenases: Evidence for a lactone intermediate in the 2,3-dihydroxyphenylpropionate 1,2-dioxygenase reaction. J. Amer. Chem. Soc. 117, 7836-7837
22. Lin, G., Reid, G., and Bugg, T.D.H. (2001) Extradiol oxidative cleavage of catechols by ferrous and ferric complexes of 1,4,7-triazacyclononane: Insight into the mechanism of the extradiol catechol dioxygenases. J. Amer. Chem. Soc. 123, 5030-5039
23. Deeth, R.J. and Bugg, T.D.H. (2003) A density functional investigation of the extradiol cleavage mechanism in non-heme iron catechol dioxygenases. J. Biol. Inorg. Chem. 8, 409-418
24. Kobayashi, T., Ishida, T., Horiike, K., Takahara, Y., Numao, N., Nakazawa, A., Nakazawa, T., and Nozaki, M. (1995) Overexpression of Pseudomonas putida catechol 2,3-dioxygenase with high specific activity by genetically engineered Escherichia coli. J. Biochem. 117, 614-622
25. Vaillancourt, F.H., Han, S., Fortin, P.D., Bolin, J.T., and 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
26. Nakajima, H., Ishida, T., Tanaka, H., and Horiike, K. (2002) Accurate measurement of near-micromolar oxygen concentrations in aqueous solutions based on enzymatic extradiol cleavage of 4-chlorocatechol: Applications to improved low-oxygen experimental systems and quantitative assessment of back diffusion of oxygen from the atmosphere. J Biochem. 131, 523-531
27. Kita, A., Kita, S., Fujisawa, I., Inaka, K., Ishida, T., Horiike, K., Nozaki, M., and Miki, K. (1999) An archetypical exradiol-cleaving catecholic dioxygenase: The crystal structure of catechol 2,3-dioxygenase (metapyrocatechase) from Pseudomonas putida mt-2. Structure 7, 25-34
28. Hansch, C., Leo, A., and Taft, R.W. (1991) A survey of Hammett substituent constants and resonance and field parameters. Chem. Rev. 91, 165-195
29. Cohen, L.A. and Jones, W.M. (1963) A study of free energy relationships in hindered phenols. Linear dependence for solvation effects in ionization. J. Amer. Chem. Soc. 85, 3397-3402
30. Klecka, G.M. and Gibson, D.T. (1981) Inhibition of catechol 2,3-dioxygenae from Pseudomonas putida by 3-chlorocatechol. Appl. Environ. Microbiol. 41, 1159-1165
31. Bartels, I., Knackmuss, H., and Reineke, W. (1984) Suicide inactivation of catechol 2,3-dioxygenase from Pseudomonas putida mt-2 by 3-halocatechols. Appl. Environ. Microbiol. 47, 500-505
32. Vaillancourt, F.H., Labbé, G., Drouin, N.M., Fortin, P.D., and Eltis, L.D. (2002) The mechanism-based inactivation of 2,3-dihydroxybiphenyl 1,2-dioxygenase by catecholic substrates. J. Biol. Chem. 277, 2019-2027
33. Shu, L., Chiou, Y.M., Orville, A.M., Miller, M.A., Lipscomb, J.D., and Que, L., Jr. (1995) X-ray absorption spectroscopic studies of the Fe(II) active site of catechol 2,3-dioxygenase. Implications for the extradiol cleavage mechanism. Biochemistry 34, 6649-6659
34. Ridder, L., Briganti, F., Boersma, M.G., Boeren, S., Vis, E.H., Scozzafava, A., Veeger, C., and Rietjens, I.M.C.M. (1998) Quantitative structure/activity relationship for the rate of conversion of C4-substituted catechols by catechol-1,2-dioxygenase from Pseudomonas putida (arvilla) C1. Eur J. Biochem. 257, 92-100
35. Dorn, E. and Knackmuss, H. (1978) Chemical structure and biodegradability of halogenated aromatic compounds. Substituent effects on 1,2-dioxygenation of catechol. Biochem. J. 174, 85-94
36. Bernstein, H.J. (2000) Recent changes to RasMol, recombining the variants. Trends Biochem. Sci. 25, 453-455