Quercetinase QueD of Streptomyces sp. FLA, a monocupin dioxygenase with a preference for nickel and cobalt

Biochemistry

Volumn 47, Issue 46, 2008, Pages 12185-12196

  Merkens, Hedda ^a   Kappl, Reinhard ^b   Jakob, Roman P ^c   Schmid, Franz X ^c   Fetzner, Susanne ^a  

^a UNIVERSITY OF MÜNSTER   (Germany)

^b SAARLAND UNIVERSITY   (Germany)

^c UNIVERSITY OF BAYREUTH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AGRICULTURAL PRODUCTS; CATALYSIS; CELL GROWTH; CIRCULAR DICHROISM SPECTROSCOPY; COBALT; COBALT COMPOUNDS; COPPER; DICHROISM; ENZYMES; ESCHERICHIA COLI; FATTY ACIDS; IRON COMPOUNDS; MANGANESE; MANGANESE ALLOYS; MANGANESE COMPOUNDS; METAL REFINING; NICKEL; NICKEL ALLOYS; OPTICAL PROPERTIES; PARAMAGNETIC RESONANCE; PARAMAGNETISM; PHENOLS; TRANSITION METALS; WATER POLLUTION; ZINC;

CATALYTIC EFFICIENCIES; CELL EXTRACTS; CIRCULAR DICHROISMS; COORDINATION GEOMETRIES; DIOXYGEN; DIOXYGENASE; E. COLI; ELECTRON PARAMAGNETIC RESONANCE SPECTRUMS; FOLDED STRUCTURES; GROWTH MEDIUMS; HYPERFINE PATTERNS; HYPSOCHROMIC SHIFTS; IONIZABLE GROUPS; KINETIC CONSTANTS; METAL CENTERS; ORGANIC CHEMISTRIES; PH DEPENDENCES; PHYSIOLOGICAL CONDITIONS; QUERCETINASE; SPECTROSCOPIC DATUMS; STREPTOMYCES SP.; UV-VIS ABSORPTIONS; VALENCE STATES;

ELECTRON SPIN RESONANCE SPECTROSCOPY;

COBALT; DIOXYGENASE; NICKEL; QUERCETINASE; UNCLASSIFIED DRUG;

ARTICLE; CIRCULAR DICHROISM; ELECTRON SPIN RESONANCE; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME KINETICS; ESCHERICHIA COLI; GENE EXPRESSION; NONHUMAN; PRIORITY JOURNAL; STREPTOMYCES; ULTRAVIOLET SPECTROSCOPY;

BACTERIAL PROTEINS; CATALYSIS; CATALYTIC DOMAIN; CIRCULAR DICHROISM; COBALT; DIOXYGENASES; ELECTRON SPIN RESONANCE SPECTROSCOPY; ESCHERICHIA COLI; GENE EXPRESSION; MODELS, CHEMICAL; NICKEL; PROTEIN STRUCTURE, SECONDARY; RECOMBINANT PROTEINS; STREPTOMYCES;

ESCHERICHIA COLI; STREPTOMYCES SP.;

EID: 56249096529     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi801398x     Document Type: Article

References (60)

1. Iwashina, T. (2000) The structure and distribution of the flavonoids in plants. J. Plant Res. 113, 287-299.
2. Pietta, P.-G. (2000) Flavonoids as antioxidants. J. Nat. Prod. 63, 1035-1042.
3. Cushnie, T. P. T., and Lamb, A. J. (2005) Antimicrobial activity of flavonoids. Int. J. Antimicrob. Agents 26, 343-356.
4. Hartwig, U. A., Joseph, C. M., and Phillips, D. A. (1991) Flavonoids released naturally from alfalfa seeds enhance growth rate of Rhizobium meliloti. Plant Physiol. 95, 797-803.
5. Stevens, J. F., Wollenweber, E., Ivancic, M., Hsu, V. L., Sundberg, S., and Deinzer, M. L. (1999) Leaf surface flavonoids of Chrysothamnus. Phytochemistry 51, 771-780.
6. Kalinova, J., Vrchotova, N., and Triska, J. (2007) Exudation of allelopathic substances in buckwheat (Fagopyrum esculentum Moench). J. Agric. Food Chem. 55, 6453-6459.
7. Westlake, D. W. S., Roxburgh, J. M., and Talbot, G. (1961) Microbial production of carbon monoxide from flavonoids. Nature 189, 510-511.
8. Schultz, E., Engle, F. E., and Wood, J. M. (1974) New oxygenases in degradation of flavones and flavanones by Pseudomonas putida. Biochemistry 13, 1768-1776.
9. Rao, J. R., and Cooper, J. E. (1994) Rhizobia catabolize nod gene-inducing flavonoids via C-ring fission mechanisms. J. Bacteriol. 176, 5409-5413.
10. Schneider, H., and Blaut, M. (2000) Anaerobic degradation of flavonoids by Eubacterium ramulus. Arch. Microbiol. 173, 71-75.
11. Oka, T., Simpson, F. J., and Krishnamurty, H. G. (1972) Degradation of rutin by Aspergillus flavus: Studies on specificity, inhibition, and possible reaction mechanism of quercetinase. Can. J. Microbiol. 18, 493-508.
12. Hund, H. K., Breuer, J., Lingens, F., Hüttermann, J., Kappl, R., and Fetzner, S. (1999) Flavonol 2,4-dioxygenase from Aspergillus niger DSM 821, a type 2 Cu-II-containing glycoprotein. Eur. J. Biochem. 263, 871-878.
13. Fusetti, F., Schröter, K. H., Steiner, R. A., van Noort, P. I., Pijning, T., Rozeboom, H. J., Kalk, K. H., Egmond, M. R., and Dijkstra, B. W. (2002) Crystal structure of the copper-containing quercetin 2,3-dioxygenase from Aspergillus japonicus. Structure 10, 259-268.
14. Bowater, L., Fairhurst, S. A., Just, V. J., and Bornemann, S. (2004) Bacillus subtilis YxaG is a novel Fe-containing quercetin 2,3-dioxygenase. FEBS Lett. 557, 45-48.
15. Barney, B. M., Schaab, M. R., LoBrutto, R., and Francisco, W. A. (2004) Evidence for a new metal in a known active site: Purification and characterization of an iron-containing quercetin 2,3-dioxygenase from Bacillus subtilis. Protein Expression Purif. 35, 131-141.
16. Merkens, H., Sielker, S., Rose, K., and Fetzner, S. (2007) A new monocupin quercetinase of Streptomyces sp. FLA: Identification and heterologous expression of the queD gene and activity of the recombinant enzyme towards different flavonols. Arch. Microbiol. 187, 475-487.
17. Tranchimand, S., Ertel, G., Gaydou, V., Gaudin, C., Tron, T., and Iacazio, G. (2008) Biochemical and molecular characterization of a quercetinase from Penicillium olsonii. Biochimie 90, 781-789.
18. Gopal, B., Madan, L. L., Betz, S. F., and Kossiakoff, A. A. (2005) The crystal structure of a quercetin 2,3-dioxygenase from Bacillus subtilis suggests modulation of enzyme activity by a change in the metal ion at the active site(s). Biochemistry 44, 193-201.
19. Dunwell, J. M., Purvis, A., and Khuri, S. (2004) Cupins: The most functionally diverse protein superfamily? Phytochemistry 65, 7-17.
20. Kooter, I. M., Steiner, R. A., Dijkstra, B. W., van Noort, P. I., Egmond, M. R., and Huber, M. (2002) EPR characterization of the mononuclear Cu-containing Aspergillus japonicus quercetin 2,3-dioxygenase reveals dramatic changes upon anaerobic binding of substrates. Eur. J. Biochem. 269, 2971-2979.
21. Schaab, M. R., Barney, B. M., and Francisco, W. A. (2006) Kinetic and spectroscopic studies on the quercetin 2,3-dioxygenase from Bacillus subtilis. Biochemistry 45, 1009-1016.
22. Dai, Y., Wensink, P. C., and Abeles, R. H. (1999) One protein, two enzymes. J. Biol. Chem. 274, 1193-1195.
23. Ju, T. T., Goldsmith, R. B., Chai, S. C., Maroney, M. J., Pochapsky, S. S., and Pochapsky, T. C. (2006) One protein, two enzymes revisited: A structural entropy switch interconverts the two isoforms of acireductone dioxygenase. J. Mol. Biol. 363, 823-834.
24. Pochapsky, T. C., Pochapsky, S. S., Ju, T. T., Mo, H. P., Al-Mjeni, F., and Maroney, M. J. (2002) Modeling and experiment yields the structure of acireductone dioxygenase from Klebsiella pneumoniae. Nat. Struct. Biol. 9, 966-972.
25. Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory Press, Plain view, NY.
26. Schlegel, H. G., Kaltwasser, H., and Gottschalk, G. (1961) Ein Submersverfahren zur Kultur wasserstoffoxydierender Bakterien: Wachstumsphysiologische Untersuchungen. Arch. Mikrobiol. 38, 209-222.
27. Pfennig, N. (1974) Rhodopseudomonas globiformis, sp. n., a new species of the Rhodospirillaceae. Arch. Microbiol. 100, 197-206.
28. Zor, T., and Selinger, Z. (1996) Linearization of the Bradford protein assay increases its sensitivity: Theoretical and experimental studies. Anal. Biochem. 236, 302-308.
29. Pace, C. N., Vajdos, F., Fee, L., Grimsley, G., and Gray, T. (1995) How to measure and predict the molar absorption coefficient of a protein. Protein Sci. 4, 2411-2423.
30. Laemmli, U. K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680-685.
31. Cornish-Bowden, A. (2004) Fundamentals of Enzyme Kinetics, 3rd ed., Portland Press Ltd., London.
32. Friedemann, T. E., and Haugen, G. E. (1943) Pyruvic acid. II. The determination of keto acids in blood and urine. J. Biol. Chem. 147, 415-442.
33. Andrade, M. A., Chacon, P., Merelo, J. J., and Morán, F. (1993) Evaluation of secondary structure of proteins from UV circular dichroism spectra using an unsupervised learning neural network. Protein Eng. 6, 383-390.
34. Outten, C. E., and O'Halloran, T. V. (2001) Femtomolar sensitivity of metalloregulatory proteins controlling zinc homeostasis. Science 292, 2488-2492.
35. Perczel, A., Park, K., and Fasman, G. D. (1992) Deconvolution of the circular dichroism spectra of proteins: The circular dichroism spectra of the antiparallel β-sheet in proteins. Proteins 13, 57-69.
36. Jungbluth, G., Rühling, i., and Ternes, W. (2000) Oxidation of flavonols with Cu(II), Fe(II) and Fe(III) in aqueous media. J. Chem. Soc., Perkin Trans. 2, 1946-1952.
37. Nishinaga, A., Tojo, T., Tomita, H., and Matsuura, T. (1979) Base-catalyzed oxygenolysis of 3-hydroxyflavones. J. Chem. Soc., Perkin Trans. 1, 2511-2516.
38. Escandar, G. M., and Sala, L. F. (1991) Complexing behavior of rutin and quercetin. Can. J. Chem. 69, 1994-2001.
39. Steiner, R. A., Kooter, I. M., and Dijkstra, B. W. (2002) Functional analysis of the copper-dependent quercetin 2,3-dioxygenase. 1. Ligand-induced coordination changes probed by X-ray crystallography: Inhibition, ordering effect, and mechanistic insights. Biochemistry 41, 7955-7962.
40. Steiner, R. A., Kalk, K. H., and Dijkstra, B. W. (2002) Anaerobic enzyme-substrate structures provide insight into the reaction mechanism of the copper-dependent quercetin 2,3-dioxygenase. Proc. Natl. Acad. Sci. U.S.A. 99, 16625-16630.
41. Day, A. J., Bao, Y., Morgan, M. R. A., and Williamson, G. (2000) Conjugation position of quercetin glucuronides and effect on biological activity. Free Radical Biol. Med. 29, 1234-1243.
42. Dai, Y., Pochapsky, T. C., and Abeles, R. H. (2001) Mechanistic studies of two dioxygenases in the methionine salvage pathway of Klebsiella pneumoniae. Biochemistry 40, 6379-6387.
43. Bicknell, R., Hanson, G. R., Holmquist, B., and Little, C. (1986) A spectral study of cobalt(II)-substituted Bacillus cereus phospholipase C Biochemistry 25, 4219-4223.
44. Bencini, A., Bertini, I., Canti, G., Gatteschi, D., and Luchinat, C. (1981) The EPR spectra of the inhibitor derivatives of cobalt carbonic anhydrase. J. Inorg. Biochem. 14, 81-93.
45. 2+ as a probe of coordination structure. 1. Dependence of the splitting on coordination geometry. J. Am. Chem. Soc. 107, 5245-5255.
46. Chai, S. C., Ju, T. T., Dang, M., Goldsmith, R. B., Maroney, M. J., and Pochapsky, T. C. (2008) Characterization of metal binding in the active sites of acireductone dioxygenase isoforms from Klebsiella ATCC 8724. Biochemistry 47, 2428-2438.
47. Dunn, M. F., Dietrich, H., MacGibbon, A. K. H., Koerber, S. C., and Zeppezauer, M. (1982) Investigation of intermediates and transition states in the catalytic mechanisms of active site substituted cobalt(II), nickel(II), zinc(II), and cadmium(II) horse liver alcohol dehydrogenase. Biochemistry 21, 354-363.
48. Sawyer, D. T., and Valentine, J. S. (1981) How super is superoxide? Ace Chem. Res. 14, 393-400.
49. Al-Mjeni, F., Ju, T., Pochapsky, T. C., and Maroney, M. J. (2002) XAS investigation of the structure and function of Ni in acireductone dioxygenase. Biochemistry 41, 6761-6769.
50. Maroney, M. J. (1999) Structure/function relationships in nickel metallobiochemistry. Curr. Opin. Chem. Biol. 3, 188-199.
51. Scarpellini, M., Wu, A. J., Kampf, J. W., and Pecoraro, V. L. (2005) Corroborative models of the cobalt(II) inhibited Fe/Mn superoxide dismutases. Inorg. Chem. 44, 5001-5010.
52. Jovanovic, S. V., Steenken, S., Hara, Y., and Simic, M. G. (1996) Reduction potentials of flavonoid and model phenoxyl radicals. Which ring in flavonoids is responsible for antioxidant activity. J. Chem. Soc., Perkin Trans. 2, 2497-2504.
53. Kaizer, J., Balogh-Hergovich, E., Czaun, M., Csay, T., and Speier, G. (2006) Redox and nonredox metal assisted model systems with relevance to flavonol and 3-hydroxyquinolin-4(1H)-one 2,4-dioxygenase. Coord Chem. Rev. 250, 2222-2233.
54. Nishinaga, A., Tojo, T., and Matsuura, T. (1974) A model catalytic oxygenation for the reaction of quercetinase. J. Chem. Soc., Chem. Commun., 896-897.
55. Nishinaga, A., Kuwashige, T., Tsutsui, T., Mashino, T., and Maruyama, K. (1994) On the mechanism of a model quercetinase reaction using a cobalt Schiff-base complex. J. Chem. Soc., Dalton Trans., 805-810.
56. Nishinaga, A., and Matsuura, T. (1973) Base-catalyzed autoxidation of 3,4′-dihydroxyflavone. J. Chem. Soc., Chem. Commun., 9-10.
57. Fetzner, S. (2002) Oxygenases without requirement for cofactors or metal ions. Appl. Microbiol. Biotechnol. 60, 243-257.
58. Frerichs-Deeken, U., Ranguelova, K., Kappl, R., Hüttermann, J., and Fetzner, S. (2004) Dioxygenases without requirement for cofactors, and their chemical model reaction: Compulsory order ternary complex mechanism of 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase involving general base catalysis by histidine 251 and single-electron oxidation of the substrate dianion. Biochemistry 43, 14485-14499.
59. Widboom, P. F., Fielding, E. N., Liu, Y., and Braner, S. D. (2007) Structural basis for cofactor-independent dioxygenation in vancomycin biosynthesis. Nature 447, 342-345.
60. Fetzner, S. (2007) Cofactor-independent oxygenases go it alone. Nat. Chem. Biol. 3, 374-375.