An archetypical extradiol-cleaving catecholic dioxygenase: The crystal structure of catechol 2,3-dioxygenase (metapyrocatechase) from Pseudomonas putida mt-2

Structure

Volumn 7, Issue 1, 1999, Pages 25-34

  Kita, Akiko ^a   Kita, Shin ichi ^a,b   Fujisawa, Ikuhide ^a   Inaka, Koji ^b   Ishida, Tetsuo ^c   Horiike, Kihachiro ^c   Nozaki, Mitsuhiro ^c   Miki, Kunio ^a  

^a KYOTO UNIVERSITY   (Japan)

^b TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

^c SHIGA UNIVERSITY OF MEDICAL SCIENCE   (Japan)

Author keywords

Catechol 2,3 dioxygenase; Extradiol dioxygenase; Metapyrocatechase; Non heme iron dioxygenase; X ray crystallography

Indexed keywords

2,3 DIHYDROXYBIPHENYL 1,2 DIOXYGENASE; CATECHOL 2,3 DIOXYGENASE; HISTIDINE; UNCLASSIFIED DRUG;

ARTICLE; CRYSTAL STRUCTURE; ENZYME ANALYSIS; ENZYME DEGRADATION; ENZYME MECHANISM; GENE DUPLICATION; NONHUMAN; PRIORITY JOURNAL; PSEUDOMONAS PUTIDA; STRUCTURE ANALYSIS; THREE DIMENSIONAL IMAGING;

EID: 0033556265     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(99)80006-9     Document Type: Article

References (36)

1. Kojima, Y., Itada, N. & Hayaishi, O. (1961). Metapyrocatechase: A new catechol-cleaving enzyme. J. Biol. Chem. 236, 2223-2228.
2. Tatsuno, Y., Saeki, Y., Nozaki, M., Otsuka, S. & Maeda, Y. (1980). Mossbauer spectra of metapyrocatechase. FEBS Lett. 112, 83-85.
3. Nakai, C., Hori, K., Kagamiyama, H., Nakazawa, T. & Nozaki, M. (1983). Purification, subunit structure, and partial amino acid sequence of metapyrocatechase. J. Biol. Chem. 258, 2916-2922.
4. Nakai, C., et al., & Nakazawa, A. (1983). Complete nucleotide sequence of the metapyrocatechase gene on the TOL plasmid of pseudomonas putida mt-2. J. Biol. Chem. 258, 2923-2928.
5. Nozaki, M., Kagamiyama, H. & Hayaishi, O. (1963). Metapyrocatechase. I. Purification, crystallization and some properties. Biochem. Z. 338, 582-590.
6. Nozaki, M., Ono, K., Nakazawa, T., Kotani, S. & Hayaishi, O. (1968). Metapyrocatechase. II. The role of iron and sulfhydryl groups. J. Biol. Chem. 243, 2682-2690.
7. Kobayashi T., et al., & 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.
8. Ohlendorf, D.H., Lipscomb, J.D. & Weber, P.C. (1988). Structure and assembly of protocatechuate 3,4-dioxygenase. Nature 336, 403-405.
9. Ohlendorf, D.H., Orville, A.M. & Lipscomb, J.D. (1994). Structure of protocatechuate 3,4-dioxygenase from Pseudomonas aeruginosa at 2.15 Å resolution. J. Mol. Biol. 244, 586-608.
10. Boyington, J.C., Gaffney, B.J. & Amzel, L.M. (1993). The three-dimensional structure of an arachidonic acid 15-lipoxygenase. Science 260, 1482-1486.
11. Han, S., Eltis, L.D., Timmis, K.N., Muchmore, S.W. & Bolin, J.T. (1995). Crystal structure of the biphenyl-cleaving extradiol dioxygenase from a PCB-degrading pseudomonad. Science 270, 976-980.
12. Senda, T., et al., & Mitsui, Y. (1996). Three-dimensional structure 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. 255, 735-752.
13. Kita, A., et al., & Miki, K. (1997). Crystallization and preliminary X-ray diffraction studies of expressed Pseudomonas putida catechol 2,3-dioxygenase. J. Biochem. 122, 201-204.
14. Bergdoll, M., Eltis, L.D., Cameron, A.D., Dumas, P. & Bolin, J.T. (1998). All in the family: Structural and evolutionary relationships among three modular proteins with diverse functions and variable assembly. Protein Sci. 7, 1661-1670.
15. Bertini, I., Briganti, F., Mangani, S., Nolting, H.F. & Scozzafava, A. (1994). X-ray absorption studies on catechol 2,3-dioxygenase from pseudomonas putida mt-2. Biochemistry 33, 10777-10784.
16. Shu, L., Chiou, Y.-M., Orville, A.M., Miller, M.A., Lipscomb, J.D. & 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.
17. Nozaki, M., Kotani, S., Ono, K. & Senoh, S. (1970). Metapyrocatechase. III. Substrate specificity and mode of ring fission. Biochim. Biophys. Acta 220, 213-223.
18. Mabrouk, P.A., Orville, A.M., Lipscomb, J.D. & Solomon, E.I. (1991). Variable-temperature variable-field magnetic circular dichroism studies of the Fe(II) active site in metapyrocatechase: Implication for the molecular mechanism of extradiol dioxygenases. J. Am. Chem. Soc. 113, 4053-4061.
19. Horiike, K., Kobayashi, T., Ishida, T. & Nozaki, M. (1991). O-Nitrophenol as an active site probe for catechol 2,3-dioxygenase. In International Symposium on Oxygenases and Oxygen Activation. (Yamamoto, S., Nozaki, M. & Ishimura, Y., eds), pp. 15-18, Yamada Science Foundation, Osaka, Japan.
20. Honjo, M., Ishida, T. & Horiike, K. (1997). Semi-micro-scale frontal gel chromatography of interacting systems of a protein and small molecules: Binding of warfarin, tryptophan, or FMN to albumin, and o-nitrophenol to catechol 2,3-dioxygenase. J. Biochem. 122, 258-263.
21. Que, L.Jr. & Ho, R.Y.N. (1996). Dioxygen activation by enzymes with mononuclear non-heme iron active sites. Chem. Rev. 96, 2607-2624.
22. Eltis, L.D. & Bolin, J.T. (1996). Evolutionary relationships among extradiol dioxygenases. J. Bacteriol. 178, 5930-5937.
23. Sakabe, N. (1991). X-ray diffraction data collection system for modern protein crystallography with Weissenberg camera and imaging plate using synchrotron radiation. Nucl. Instrum. Methods A 303, 448-463.
24. Miyahara, J., Takahashi, K., Amemiya, Y., Kamiya, N. & Satow, Y. (1986). A new type of X-ray area detector utilizing laser stimulated luminescence. Nucl. Instrum. Methods A 246, 572-578.
25. Higashi, T. (1989). The processing of diffraction data taken on a screenless Weissenberg camera for macromolecular crystallography. J. Appl. Cryst. 22, 9-18.
26. Otwinowski, Z. & Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode. In Methods in Enzymology Vol. 276. (Carter, C.W. Jr. & Sweet, R.M., eds), pp. 307-326, Academic Press, New York, NY.
27. Steigemann, W. (1992). PROTEIN Version 3.1 : A Program System for the Crystal Structure Analysis of Proteins. Max-Planck Institut für Biochemie, Martinsried, Germany.
28. Cowtan, K. & Main, P. (1996). Phase combination and cross validation in iterated density-modification calculations. Acta Cryst. D 52, 43-48.
29. Collaborative Computational Project No. 4. (1994). The CCP4 suite: Programs for protein crystallography. Acta Cryst. D 50, 760-763.
30. Roussel, A. & Cambillau, C. (1989). TURBO-FRODO. In Silicon Graphics Geometry Partners Directory, pp. 77-78, Silicon Graphics, Mountain View, CA.
31. Read, R.J. (1986). Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Cryst. A 42, 140-149.
32. Brünger, A.T. (1992). X-PLOR Version 3.1 Manual. Yale University Press, New Haven, CT.
33. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. (1993). J. Appl. Cryst. 26, 283-291.
34. Kraulis, P.J. (1991 ). MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24, 946-950.
35. Merrit, E.A. & Murphy, M.E.P. (1994). Raster3D version 2.0 - A program for photorealistic molecular graphics. Acta Cryst. D 50, 869-873.
36. Nicholls, A., Sharp, K.A. & Honig, B. (1991 ). Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281-296.