Toxoflavin lyase requires a novel 1-His-2-carboxylate facial triad

Biochemistry

Volumn 50, Issue 6, 2011, Pages 1091-1100

  Fenwick, Michael K ^a   Philmus, Benjamin ^b   Begley, Tadhg P ^b   Ealick, Steven E ^a  

^a Department of Obstetrics Gynecology   (United States)

^b TEXAS A AND M UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHELATION; CHEMICAL ACTIVATION; CRYSTAL STRUCTURE; ENZYMES; MANGANESE COMPOUNDS; METALS; OXYGEN;

COORDINATION SITES; DEGRADATION REACTION; HIGH RESOLUTION CRYSTAL STRUCTURE; METAL BINDING SITES; REDUCTIVE ACTIVATION; SEQUENCE IDENTITY; SQUARE-PYRAMIDAL GEOMETRY; STRUCTURAL MODULE;

IRON COMPOUNDS;

CARBOXYLIC ACID DERIVATIVE; HISTIDINE DERIVATIVE; LYASE; MANGANESE; OXYGEN; TOXOFLAVIN DEGRADING METALLOENZYME; TOXOFLAVIN LYASE; UNCLASSIFIED DRUG; WATER;

ARTICLE; BINDING SITE; BIOCHEMISTRY; CRYSTAL STRUCTURE; CRYSTALLIZATION; ENZYME ACTIVITY; ENZYME INACTIVATION; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; METAL BINDING; MOLECULAR INTERACTION; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN FOLDING; PROTEIN PURIFICATION; PROTEIN STRUCTURE; SYNTHESIS;

EID: 79851487499     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi101741v     Document Type: Article

References (54)

1. Levenberg, B. and Linton, S. N. (1966) On the biosynthesis of toxoflavin, an azapteridine antibiotic produced by Pseudomonas cocovenenans J. Biol. Chem. 241, 846-852
2. Lynch, K. H. and Dennis, J. J. (2010) Burkholderia. In Molecular detection of foodborne pathogens (Liu, D., Ed.) pp 331 - 343, CRC Press, Boca Raton, FL.
3. Latuasan, H. E. and Berends, W. (1961) On the origin of the toxicity of toxoflavin Biochim. Biophys. Acta 52, 502-508
4. Stern, K. G. (1935) Oxidation-reduction potentials of toxoflavin Biochem. J. 29, 500-508
5. Goto, K. and Ohata, K. (1956) New bacterial diseases of rice (brown stripe and grain rot) Nippon Shokubutsu Byori Gakkaiho 21, 46-47
6. Jeong, Y., Kim, J., Kim, S., Kang, Y., Nagamatsu, T., and Hwang, I. (2003) Toxoflavin produced by Burkholderia glumae causing rice grain rot is responsible for inducing bacterial wilt in many field crops Plant Dis. 87, 890-895
7. Nandakumar, R., Shahjahan, A. K. M., Yuan, X. L., Dickstein, E. R., Groth, D. E., Clark, C. A., Cartwright, R. D., and Rush, M. C. (2009) Burkholderia glumae and B. gladioli cause bacterial panicle blight in rice in the southern United States Plant Dis. 93, 896-905
8. Uematsu, T., Yoshimura, D., Nishiyama, K., Ibaraki, T., and Fujii, H. (1976) Pathogenic bacterium causing seedling rot of rice Nippon Shokubutsu Byori Gakkaiho 42, 464-471
9. Hwang, I. G., Moon, J. S., and Jwa, N. S. (2009) TflA gene which can degrade toxoflavin and its chemical derivatives and transgenic organisms expressing TflA gene. Organization, W. I. P., Ed.
10. Armstrong, R. N. (2000) Mechanistic diversity in a metalloenzyme superfamily Biochemistry 39, 13625-13632
11. Babbitt, P. C. and Gerlt, J. A. (1997) Understanding enzyme superfamilies. Chemistry as the fundamental determinant in the evolution of new catalytic activities J. Biol. Chem. 272, 30591-30594
12. Bergdoll, M., Eltis, L. D., Cameron, A. D., Dumas, P., and 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
13. Gerlt, J. A. and Babbitt, P. C. (2001) Divergent evolution of enzymatic function: Mechanistically diverse superfamilies and functionally distinct suprafamilies Annu. Rev. Biochem. 70, 209-246
14. Que, L., Jr. (2000) One motif: Many different reactions Nat. Struct. Biol. 7, 182-184 (Pubitemid 30140757)
15. Laemmli, U. K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4 Nature 227, 680-685
16. 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
17. Otwinowski, Z. and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. In Methods in Enzymology (Carter, C. W., Jr. and Sweet, R. M., Eds.) pp 307 - 326, Academic Press, New York. (Pubitemid 27085611)
18. Schneider, T. R. and Sheldrick, G. M. (2002) Substructure solution with SHELXD Acta Crystallogr. D58, 1772-1779
19. Sheldrick, G. M. (2008) A short history of SHELX Acta Crystallogr. A64, 112-122
20. Adams, P. D., Afonine, P. V., BunkoÌczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L.-W., Kapral, G. J., Grosse-Kunstleve, R. W., McCoy, A. J., Moriarty, N. W., Oeffner, R., Read, R. J., Richardson, D. C., Richardson, J. S., Terwilliger, T. C., and Zwart, P. H. (2010) PHENIX: A comprehensive Python-based system for macromolecular structure solution Acta Crystallogr. D66, 213-221
21. Emsely, P., Lohkamp, B., Scott, W. G., and Cowtan, K. (2010) Features and development of Coot Acta Crystallogr. D66, 486-501
22. Moriarty, N. W., Grosse-Kunstleve, R. W., and Adams, P. D. (2009) electronic Ligand Builder and Optimization Workbench (eLBOW): A tool for ligand coordinate and restraint generation Acta Crystallogr. D65, 1074-1080
23. Word, J. M., Lovell, S. C., Richardson, J. S., and Richardson, D. C. (1999) Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation J. Mol. Biol. 285, 1735-1747
24. Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) PROCHECK: A program to check the stereochemical quality of protein structures J. Appl. Crystallogr. 26, 283-291
25. Black, T. H. (1987) An improved, large-scale synthesis of xanthothricin and reumycin J. Heterocycl. Chem. 24, 1373-1375 (Pubitemid 17144728)
26. Goddard, T. D., Huang, C. C., and Ferrin, T. E. (2007) Visualizing density maps with UCSF Chimera J. Struct. Biol. 157, 281-287
27. Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., and Ferrin, T. E. (2004) UCSF Chimera: A visualization system for exploratory research and analysis J. Comput. Chem. 25, 1605-1612
28. Berman, H. M., Battistuz, T., Bhat, T. N., Bluhm, W. F., Bourne, P. E., Burkhardt, K., Feng, Z., Gilliland, G. L., Iype, L., Jain, S., Fagan, P., Marvin, J., Padilla, D., Ravichandran, V., Schneider, B., Thanki, N., Weissig, H., Westbrook, J. D., and Zardecki, C. (2002) The Protein Data Bank Acta Crystallogr. D58, 899-907
29. Holm, L. and Rosenstrom, P. (2010) Dali server: Conservation mapping in 3D Nucleic Acids Res. 38 (Suppl.) W545-W549
30. Cameron, A. D., Olin, B., Ridderstrom, M., Mannervik, B., and Jones, T. A. (1997) Crystal structure of human glyoxalase I: Evidence for gene duplication and 3D domain swapping EMBO J. 16, 3386-3395
31. He, M. M., Clugston, S. L., Honek, J. F., and Matthews, B. W. (2000) Determination of the structure of Escherichia coli glyoxalase I suggests a structural basis for differential metal activation Biochemistry 39, 8719-8727
32. McCarthy, A. A., Baker, H. M., Shewry, S. C., Patchett, M. L., and Baker, E. N. (2001) Crystal structure of methylmalonyl-coenzyme A epimerase from P. shermanii: A novel enzymatic function on an ancient metal binding scaffold Structure 9, 637-646
33. + J. Am. Chem. Soc. 124, 11001-11003
34. Han, S., Eltis, L. D., Timmis, K. N., Muchmore, S. W., and Bolin, J. T. (1995) Crystal structure of the biphenyl-cleaving extradiol dioxygenase from a PCB-degrading pseudomonad Science 270, 976-980
35. Kita, A., Kita, S., Fujisawa, I., Inaka, K., Ishida, T., Horiike, K., Nozaki, M., and Miki, K. (1999) An archetypical extradiol-cleaving catecholic dioxygenase: The crystal structure of catechol 2,3-dioxygenase (metapyrocatechase) from Pseudomonas putida mt-2 Structure 7, 25-34
36. Senda, T., Sugiyama, K., Narita, H., Yamamoto, T., Kimbara, K., Fukuda, M., Sato, M., Yano, K., and Mitsui, Y. (1996) 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. 255, 735-752
37. Vetting, M. W., Wackett, L. P., Que, L., Jr., Lipscomb, J. D., and Ohlendorf, D. H. (2004) Crystallographic comparison of manganese- and iron-dependent homoprotocatechuate 2,3-dioxygenases J. Bacteriol. 186, 1945-1958
38. Brownlee, J. M., Johnson-Winters, K., Harrison, D. H., and Moran, G. R. (2004) Structure of the ferrous form of (4-hydroxyphenyl)pyruvate dioxygenase from Streptomyces avermitilis in complex with the therapeutic herbicide, NTBC Biochemistry 43, 6370-6377
39. Serre, L., Sailland, A., Sy, D., Boudec, P., Rolland, A., Pebay-Peyroula, E., and Cohen-Addad, C. (1999) Crystal structure of Pseudomonas fluorescens 4-hydroxyphenylpyruvate dioxygenase: An enzyme involved in the tyrosine degradation pathway Structure 7, 977-988
40. Dumas, P., Bergdoll, M., Cagnon, C., and Masson, J. M. (1994) Crystal structure and site-directed mutagenesis of a bleomycin resistance protein and their significance for drug sequestering EMBO J. 13, 2483-2492
41. Saint-Jean, A. P., Phillips, K. R., Creighton, D. J., and Stone, M. J. (1998) Active monomeric and dimeric forms of Pseudomonas putida glyoxalase I: Evidence for 3D domain swapping Biochemistry 37, 10345-10353
42. Cunningham, B. A., Hemperly, J. J., Hopp, T. P., and Edelman, G. M. (1979) Favin versus concanavalin A: Circularly permuted amino acid sequences Proc. Natl. Acad. Sci. U.S.A. 76, 3218-3222
43. Lindqvist, Y. and Schneider, G. (1997) Circular permutations of natural protein sequences: Structural evidence Curr. Opin. Struct. Biol. 7, 422-427
44. Gerlt, J. A. and Babbitt, P. C. (1998) Mechanistically diverse enzyme superfamilies: The importance of chemistry in the evolution of catalysis Curr. Opin. Chem. Biol. 2, 607-612
45. Laughlin, L. T., Bernat, B. A., and Armstrong, R. N. (1998) Mechanistic imperative for the evolution of a metalloglutathione transferase of the vicinal oxygen chelate superfamily Chem.-Biol. Interact. 111-112, 41-50
46. Koehntop, K. D., Emerson, J. P., and Que, L., Jr. (2005) The 2-His-1-carboxylate facial triad: A versatile platform for dioxygen activation by mononuclear non-heme iron(II) enzymes J. Biol. Inorg. Chem. 10, 87-93
47. Vaillancourt, F. H., Bolin, J. T., and Eltis, L. D. (2006) The ins and outs of ring-cleaving dioxygenases Crit. Rev. Biochem. Mol. Biol. 41, 241-267
48. He, P. and Moran, G. R. (2009) We two alone will sing: The two-substrate α-keto acid-dependent oxygenases Curr. Opin. Chem. Biol. 13, 443-450
49. Fagan, R. L. and Palfey, B. A. (2010) Flavin-Dependent Enzymes. In Comprehensive Natural Products II (Lew, M. and Hung-Wen, L., Eds.) pp 37 - 113, Elsevier, Oxford, U.K.
50. 5-phenethylflavins J. Am. Chem. Soc. 102, 5036-5044
51. 18O-Labeled Guanidinohydantoin from Guanosine Oxidation with Singlet Oxygen. Implications for Structure and Mechanism J. Am. Chem. Soc. 125, 13926-13927
52. Bassan, A., Blomberg, M. R. A., and Siegbahn, P. E. M. (2003) Mechanism of dioxygen cleavage in tetrahydrobiopterin-dependent amino acid hydroxylases Chem. - Eur. J. 9, 106-115
53. Mukherjee, T., Zhang, Y., Abdelwahed, S., Ealick, S. E., and Begley, T. P. (2010) Catalysis of a Flavoenzyme-Mediated Amide Hydrolysis J. Am. Chem. Soc. 132, 1550-1551
54. Kabsch, W. and Sander, C. (1983) Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features Biopolymers 22, 2577-2637