Structural and biochemical characterization of gentisate 1,2-dioxygenase from Escherichia coli O157:H7

Molecular Microbiology

Volumn 61, Issue 6, 2006, Pages 1469-1484

  Adams, Melanie A ^a   Singh, Vinay K ^a   Keller, Bernd O ^a   Jia, Zongchao ^a  

^a QUEEN S UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BENZOIC ACID DERIVATIVE; CALCIUM SULFATE; CARBON; COPPER; DIOXYGENASE; EDETIC ACID; GENTISIC ACID; IRON; LITHIUM SULFATE; MAGNESIUM SULFATE; MANGANESE; POTASSIUM; SODIUM SULFATE; TETRAMER; ZINC;

AMINO ACID SEQUENCE; ARTICLE; CHEMICAL ANALYSIS; CONTROLLED STUDY; DEGRADATION; ENTEROHEMORRHAGIC ESCHERICHIA COLI; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME STRUCTURE; ESCHERICHIA COLI; NONHUMAN; OPERON; PATHOGENIC ESCHERICHIA COLI; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN MOTIF; SEQUENCE ANALYSIS; SHIGA TOXIN PRODUCING ESCHERICHIA COLI; STRESS; TANDEM MASS SPECTROMETRY;

AMINO ACID SEQUENCE; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DIOXYGENASES; ESCHERICHIA COLI O157; ESCHERICHIA COLI PROTEINS; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 33748498955     PISSN: 0950382X     EISSN: 13652958     Source Type: Journal    
DOI: 10.1111/j.1365-2958.2006.05334.x     Document Type: Article

References (72)

1. Adams, M., and Jia, Z. (2005) Structural and biochemical analysis reveal pirins to possess quercetinase activity. J Biol Chem 280: 28675-28682.
2. Adams, P.D., Grosse-Kunstleve, R.W., Hung, L.W., Ioerger, T.R., McCoy, A.J., Moriarty, N.W., et al. (2002) PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr D Biol Crystallogr 58: 1948-1954.
3. Andreeva, A., Howorth, D., Brenner, S.E., Hubbard, T.J., Chothia, C., and Murzin, A.G. (2004) SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res 32: D226-D229.
4. Bayly, R.C., Chapman, P.J., Dagley, S., and Di Berardino, D. (1980) Purification and some properties of maleylpyruvate hydrolase and fumarylpyruvate hydrolase from Pseudomonas alcaligenes. J Bacteriol 143: 70-77.
5. Bradford, M.M. (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72: 248-254.
6. Brooks, S.P. (1992) A simple computer program with statistical tests for the analysis of enzyme kinetics. Biotechniques 13: 906-911.
7. Bruckner, R., and Titgemeyer, F. (2002) Carbon catabolite repression in bacteria: choice of the carbon source and autoregulatory limitation of sugar utilization. FEMS Microbiol Lett 209: 141-148.
8. Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., et al. (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 54: 905-921.
9. Cheary, R.W., and Coelho, A.A. (1996) Programs XFIT and FOURYA. CCP14 Powder Diffraction Library. Daresbury Laboratory, Warrington, England, Engineering and Physical Sciences Research Council.
10. Chua, C.H., Feng, Y., Yeo, C.C., Khoo, H.E., and Poh, C.L. (2001) Identification of amino acid residues essential for catalytic activity of gentisate 1,2-dioxygenase from Pseudomonas alcaligenes NCIB 9867. FEMS Microbiol Lett 204: 141-146.
11. Crawford, R.L. (1975) Degradation of 3-hydroxybenzoate by bacteria of the genus Bacillus. Appl Microbiol 30: 439-444.
12. Crawford, R.L. (1976) Pathways of 4-hydroxybenzoate degradation among species of Bacillus. J Bacteriol 127: 204-210.
13. Crawford, R.L., and Frick, T.D. (1977) Rapid spectrophotometric differentiation between glutathione-dependent and glutathione-independent gentisate and homogentisate pathways. Appl Environ Microbiol 34: 170-174.
14. Crawford, R.L., Hutton, S.W., and Chapman, P.J. (1975) Purification and properties of gentisate 1,2-dioxygenase from Moraxella osloensis. J Bacteriol 121: 794-799.
15. Dagley, S. (1975) A biochemical approach to some problems of environmental pollution. Essays Biochem 11: 81-138.
16. Dunwell, J.M. (1998) Sequence analysis of the cupin gene family in Synechocystis PCC6803. Microb Comp Genomics 3: 141-148.
17. Elliott, S.J., Wainwright, L.A., McDaniel, T.K., Jarvis, K.G., Deng, Y.K., Lai, L.C., et al. (1998) The complete sequence of the locus of enterocyte effacement (LEE) from enteropathogenic Escherichia coli E2348/69. Mol Microbiol 28: 1-4.
18. Feng, Y., Khoo, H.E., and Poh, C.L. (1999) Purification and characterization of gentisate 1,2-dioxygenases from Pseudomonas alcaligenes NCIB 9867 and Pseudomonas putida NCIB 9869. Appl Environ Microbiol 65: 946-950.
19. Fruth, A., Prager, R., Friedrich, A., Kuczius, T., Roggentin, P., Karch, H., et al. (2005) ESEC infections in humans in the Federal Republic of Germany, 1998-2001. Prevalence and types of pathogens. Gesundheitsschutz 45: 715-721.
20. Fuenmayor, S.L., Wild, M., Boyes, A.L., and Williams, P.A. (1998) A gene cluster encoding steps in conversion of naphthalene to gentisate in Pseudomonas sp. strain U2. J Bacteriol 180: 2522-2530.
21. Fusetti, F., Schroter, K.H., Steiner, R.A., van Noort, P.I., Pijning, T., Rozeboom, H.J., et al. (2002) Crystal structure of the copper-containing quercetin 2,3-dioxygenase from Aspergillus japonicus. Structure (Camb) 10: 259-268.
22. Grosse-Kunstleve, R.W., and Adams, P.D. (2003) Substructure search procedures for macromolecular structures. Acta Crystallogr D Biol Crystallogr 59: 1966-1973.
23. Hacker, J., Blum-Oehler, G., Muhldorfer, I., and Tschape, H. (1997) Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution. Mol Microbiol 23: 1089-1097.
24. Harpel, M.R., and Lipscomb, J.D. (1990a) Gentisate 1,2-dioxygenase from pseudomonas. Purification, characterization, and comparison of the enzymes from Pseudomonas testosteroni and Pseudomonas acidovorans. J Biol Chem 265: 6301-6311.
25. 2+ and mechanism of turnover. J Biol Chem 265: 22187-22196.
26. Hendrickson, W.A., Horton, J.R., and LeMaster, D.M. (1990) Selenomethionyl proteins produced for analysis by multi-wavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure. EMBO J 9: 1665-1672.
27. Hintner, J.P., Reemtsma, T., and Stolz, A. (2004) Biochemical and molecular characterization of a ring fission dioxygenase with the ability to oxidize (substituted) salicylate(s) from Pseudaminobacter salicylatoxidans. J Biol Chem 279: 37250-37260.
28. Ingraham, J.L., and Neidhardt, F.C. (1987) Escherichia coli & Salmonella typhimurium: Cellular & Molecular Biology. Washington, DC: American Society for Microbiology.
29. Jores, J., Rumer, L., Kiessling, S., Kaper, J.B., and Wieler, L.H. (2001) A novel locus of enterocyte effacement (LEE) pathogenicity island inserted at pheV in bovine Shiga toxin-producing Escherichia coli strain O103:H2. FEMS Microbiol Lett 204: 75-79.
30. Jores, J., Rumer, L., and Wieler, L.H. (2004) Impact of the locus of enterocyte effacement pathogenicity island on the evolution of pathogenic Escherichia coli. Int J Med Microbiol 294: 103-113.
31. Jores, J., Wagner, S., Rumer, L., Eichberg, J., Laturnus, C., Kirsch, P., et al. (2005) Description of a 111-kb pathogenicity island (PAI) encoding various virulence features in the enterohemorrhagic E. coli (EHEC) strain RW1374 (O103:H2) and detection of a similar PAI in other EHEC strains of serotype 0103:H2. Int J Med Microbiol 294: 417-425.
32. Karaolis, D.K., McDaniel, T.K., Kaper, J.B., and Boedeker, E.C. (1997) Cloning of the RDEC-1 locus of enterocyte effacement (LEE) and functional analysis of the phenotype on HEp-2 cells. Adv Exp Med Biol 412: 241-245.
33. Knox, W.E., and Edwards, S.W. (1955) Homogentisate oxidase of liver. J Biol Chem 216: 479-487.
34. Krissinel, E., and Henrick, K. (2003) Protein structure comparison in 3D based on secondary structure matching (SSM) followed by Ca alignment, scored by a new structural similarity function. In Proceedings of the 5th International Conference on Molecular Structural Biology, Vienna, 88, 3 September 2003. Kungl, A.J., and Kungl, P.J. (eds).
35. La Du, B.N., Zannoni, V.G., Laster, L., and Seegmiller, J.E. (1958) The nature of the defect in tyrosine metabolism in alcaptonuria. J Biol Chem 230: 251-260.
36. Lack, L. (1959) The enzymic oxidation of gentisic acid. Biochim Biophys Acta 34: 117-123.
37. Lack, L. (1961) Enzymic cis-trans isomerization of maleylpyruvic acid. J Biol Chem 236: 2835-2840.
38. Ladd, J.N. (1962) Oxidation of anthranilic acid by a species of Achromobacter isolated from soil. Nature 194: 1099-1100.
39. McDaniel, T.K., Jarvis, K.G., Donnenberg, M.S., and Kaper, J.B. (1995) A genetic locus of enterocyte effacement conserved among diverse enterobacterial pathogens. Proc Natl Acad Sci USA 92: 1664-1668.
40. McRee, D.E. (1992) A visual protein crystallographic software system for X11/Xview. J Mol Graphics 10: 44-46.
41. Mekalanos, J.J. (1992) Environmental signals controlling expression of virulence determinants in bacteria. J Bacteriol 174: 1-7.
42. Morris, G.M., Goodsell, D.S., Halliday, R.S., Huey, R., Hart, W.E., Belew, R.K., and Olson, A.J. (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19: 1639-1662.
43. Murshudov, G.N., Vagub, A.A., and Dodson, E.J. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr D53: 240-255.
44. O'Brien, W.M., La Du, B.N., and Bunim, J.J. (1963) Biochemical, pathologic and clinical aspects of alcaptonuria, ochronosis and ochronotic arthropathy: review of world literature (1584-1962). Am J Med 34: 813-838.
45. Otwinowski, Z., and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276: 307-326.
46. Pang, H., Bartlam, M., Zeng, Q., Miyatake, H., Hisano, T., Miki, K., et al. (2004) Crystal structure of human pirin: an iron-binding nuclear protein and transcription cofactor. J Biol Chem 279: 1491-1498.
47. Perna, N.T., Mayhew, G.F., Posfai, G., Elliott, S., Donnenberg, M.S., Kaper, J.B., and Blattner, F.R. (1998) Molecular evolution of a pathogenicity island from enterohemorrhagic Escherichia coli O157:H7. Infect Immun 66: 3810-3817.
48. Que, L., Jr, and Ho, R.Y. (1996) Dioxygen activation by enzymes with mononuclear non-heme iron active sites. Chem Rev 96: 2607-2624.
49. Rani, M., Prakash, D., Sobti, R.C., and Jain, R.K. (1996) Plasmid-mediated degradation of o-phthalate and salicylate by a Moraxella sp. Biochem Biophys Res Commun 220: 377-381.
50. Ribbons, D.W. (1970) Stoicheiometry of O-demethylase activity in Pseudomonas aeruginosa. FEBS Lett 8: 101-104.
51. Rumer, L., Jores, J., Kirsch, P., Cavignac, Y., Zehmke, K., and Wieler, L.H. (2003) Dissemination of pheU- and pheV-located genomic islands among enteropathogenic (EPEC) and enterohemorrhagic (EHEC) E. coli and their possible role in the horizontal transfer of the locus of enterocyte effacement (LEE). Int J Med Microbiol 292: 463-475.
52. Schmidt, H., Geitz, C., Tarr, P.I., Frosch, M., and Karch, H. (1999) Non-O157:H7 pathogenic Shiga toxin-producing Escherichia coli: phenotypic and genetic profiling of virulence traits and evidence for clonality. J Infect Dis 179: 115-123.
53. Shen, X.H., Jiang, C.Y., Huang, Y., Liu, Z.P., and Liu, S.J. (2005) Functional identification of novel genes involved in the glutathione-independent gentisate pathway in Corynebacterium glutamicum. Appl Environ Microbiol 71: 3442-3452.
54. Suarez, M., Ferrer, E., Garrido-Pertierra, A., and Martin, M. (1995) Purification and characterization of the 3-hydroxybenzoate-6-hydroxylase from Klebsiella pneumoniae. FEMS Microbiol Lett 126: 283-290.
55. Suarez, M., Ferrer, E., and Martin, M. (1996) Purification and biochemical characterization of gentisate 1,2-dioxygenase from Klebsiella pneumoniae M5a1. FEMS Microbiol Lett 143: 89-95.
56. Sugiyama, S.I., Yano, K., Tanaka, H., Komagata, K., and Arima, K. (1958) Metabolism of aromatic compounds by bacteria. I. Gentisic acid oxidase and protocatechuic acid oxidase of Pseudomonas ovalis S-5. J Gen Appl Microbiol 4: 223-240.
57. Sugiyama, S.I., Tanaka, H., Yano, K., and Arima, K. (1960) New pathways in the oxidative metabolism of aromatic compounds by micro-organisms. Bull Agr Chem Soc Jpn 24: 255-261.
58. Tauschek, M., Strugnell, R.A., and Robins-Browne, R.M. (2002) Characterization and evidence of mobilization of the LEE pathogenicity island of rabbit-specific strains of enteropathogenic Escherichia coli. Mol Microbiol 44: 1533-1550.
59. Terwilliger, T.C. (2000) Maximum-likelihood density modification. Acta Crystallogr D Biol Crystallogr 56: 965-972.
60. Terwilliger, T.C. (2003) Automated main-chain model building by template matching and iterative fragment extension. Acta Crystallogr D Biol Crystallogr 59: 38-44.
61. Terwilliger, T.C., and Berendzen, J. (1999) Automated MAD and MIR structure solution. Acta Crystallogr D Biol Crystallogr 55: 849-861.
62. Titus, G.P., Mueller, H.A., Burgner, J., Rodriguez, D.C., Penalva, M.A., and Timm, D.E. (2000) Crystal structure of human homogentisate dioxygenase. Nat Struct Biol 7: 542-546.
63. Tomasek, P.H., and Crawford, R.L. (1986) Initial reactions of xanthone biodegradation by an Arthrobacter sp. J Bacteriol 167: 818-827.
64. Walker, N., and Lippert, K.D. (1965) Formation of gentisic acid from 2-napthol by a Pseudomonas. Biochem J 95: 5C-6C.
65. Werwath, J., Arfmann, H.A., Pieper, D.H., Timmis, K.N., and Wittich, R.M. (1998) Biochemical and genetic characterization of a gentisate 1, 2-dioxygenase from Sphingomonas sp. strain RW5. J Bacteriol 180: 4171-4176.
66. Wieler, L.H., McDaniel, T.K., Whittam, T.S., and Kaper, J.B. (1997) Insertion site of the locus of enterocyte effacement in enteropathogenic and enterohemorrhagic Escherichia coli differs in relation to the clonal phylogeny of the strains. FEMS Microbiol Lett 156: 49-53.
67. Wittich, R.M., Rast, H.G., and Knackmuss, H.J. (1988) Degradation of naphthalene-2,6- and naphthalene-1,6-disulfonic acid by a Moraxella sp. Appl Environ Microbiol 54: 1842-1847.
68. Yano, K., and Arima, K. (1958) Metabolism of aromatic compounds by bacteria, II. m-Hydroxybenzoic acid hydroxylase A and B; 5-dehydroshikimic acid, a precursor of protocatechuic acid: a new pathway from salicylic acid to gentisic acid. J Gen Appl Microbiol 4: 241-258.
69. Yeo, C.C., Wong, M.V., Feng, Y., Song, K.P., and Poh, C.L. (2003) Molecular characterization of an inducible gentisate 1,2-dioxygenase gene, xlnE, from Pseudomonas alcaligenes NCIMB 9867. Gene 312: 239-248.
70. Yoh, M., Bi, Z., Matsuyama, J., Nagayama, K., and Honda, T. (2003) Effect of environmental conditions on proteins secreted by enterohemorrhagic Escherichia coli O26:H11. Microbiol Immunol 47: 1-6.
71. Zhou, N.Y., Fuenmayor, S.L., and Williams, P.A. (2001) nag genes of Ralstonia (formerly Pseudomonas) sp. strain U2 encoding enzymes for gentisate catabolism. J Bacteriol 183: 700-708.
72. Zhu, C., Agin, T.S., Elliott, S.J., Johnson, L.A., Thate, T.E., Kaper, J.B., and Boedeker, E.C. (2001) Complete nucleotide sequence and analysis of the locus of enterocyte effacement from rabbit diarrheagenic Escherichia coli RDEC-1. Infect Immun 69: 2107-2115.