Identification of metal binding residues for the binuclear zinc phosphodiesterase reveals identical coordination as glyoxalase II

Biochemistry

Volumn 43, Issue 32, 2004, Pages 10379-10386

  Vogel, Andreas ^a   Schilling, Oliver ^a   Meyer Klaucke, Wolfram ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ABSORPTION SPECTROSCOPY; CATALYSIS; ENZYMES; ESCHERICHIA COLI; REACTION KINETICS; ZINC;

MUTANTS; X-RAY ABSORPTION FINE STRUCTURE (XAFS);

BIOCHEMISTRY;

BETA LACTAMASE; BIS(4 NITROPHENYL) PHOSPHATE; HYDROXYACYLGLUTATHIONE HYDROLASE; MUTANT PROTEIN; PHOSPHODIESTERASE; UNCLASSIFIED DRUG; ZINC; ZINC PHOSPHODIESTERASE;

ABSORPTION SPECTROSCOPY; ARTICLE; ENZYME ACTIVE SITE; ENZYME MECHANISM; ESCHERICHIA COLI; FOURIER TRANSFORMATION; METAL BINDING; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SITE DIRECTED MUTAGENESIS;

AMINO ACID SEQUENCE; BETA-LACTAMASES; BINDING SITES; CATALYSIS; ESCHERICHIA COLI; KINETICS; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; NITROPHENOLS; PHOSPHORIC DIESTER HYDROLASES; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; SEQUENCE HOMOLOGY, AMINO ACID; SUBSTRATE SPECIFICITY; THIOLESTER HYDROLASES; X-RAYS; ZINC;

ESCHERICHIA COLI;

EID: 3142738641     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi049703+     Document Type: Article

References (40)

1. Vogel, A., Schilling, O., Niecke, M., Bettmer, J., and Meyer-Klaucke W. (2002) ElaC encodes a novel binuclear zinc phosphodiesterase, J. Biol. Chem. 277, 29078-29085.
2. Tavtigian, S. V., Simard, J., Teng, D. H., Abtin, V., Baumgard, M., Beck, A., Camp, N. J., Carillo, A. R., Chen, Y., Dayananth, P., Desrochers, M., Dumont, M., Farnham, J. M., Frank, D., Frye, C., Ghaffari, S., Gupte, J. S., Hu, R., Iliev, D., Janecki, T., Kort, E. N., Laity, K. E., Leavitt, A., Leblanc, G., McArthur-Morrison, J., Pederson, A., Penn, B., Peterson, K. T., Reid, J. E., Richards, S., Schroeder, M., Smith, R., Snyder, S. C., Swedlund, B., Swensen, J., Thomas, A., Tranchant, M., Woodland, A. M., Labrie, F., Skolnick, M. H., Neuhausen, S., Rommens, J., and Cannon-Albright, L. A. (2001) A candidate prostate cancer susceptibility gene at chromosome 17p, Nat. Genet. 27, 172-180.
3. Schiffer, S., Rosch, S., and Marchfelder, A. (2002) Assigning a function to a conserved group of proteins: the tRNA 3′-processing enzymes, EMBO J. 21, 2769-2777.
4. Takaku, H., Minagawa, A., Takagi, M., and-Nashimoto, M. (2003) A candidate prostate cancer susceptibility gene encodes tRNA 3′ processing endoribonuclease, Nucleic Acids Res. 31, 2272-2278.
5. Li, Z., and Deutscher, M. P. (2002) RNase E plays an essential role in the maturation of Escherichia coli tRNA precursors, RNA 8, 97-109.
6. Schurer, H., Schiffer, S., Marchfelder, A., and Morl, M. (2001) This is the end: processing, editing and repair at the tRNA 3′-terminus, Biol. Chem. 382, 1147-1156.
7. Pellegrini, O., Nezzar, J., Marchfelder, A., Putzer, H., and Condon, C. (2003) Endonucleolytic processing of CCA-less tRNA precursors by RNase Z in Bacillus subtilis, EMBO J. 22, 4534-4543.
8. Daiyasu, H., Osaka, K., Ishino, Y., and Toh, H. (2001) Expansion of the zinc metallo-hydrolase family of the beta-lactamase fold, FEBS Lett. 503, 1-6.
9. Aravind, L. (1999) An evolutionary classification of the metallo-beta-lactamase fold proteins, In Silica Biol. 1, 69-91.
10. Cameron, A. D., Ridderstrom, M., Olin, B., and Mannervik, B. (1999) Crystal structure of human glyoxalase II and its complex with a glutathione thiolester substrate analogue, Struct. Folding Des. 7, 1067-1078.
11. Carfi, A., Pares, S., Duee, E., Galleni, M., Duez, C., Frère, J. M., and Dideberg, O. (1995) The 3-D structure of a zinc metallo-beta-lactamase from Bacillus cereus reveals a new type of protein fold, EMBO J. 14, 4914-4921.
12. Callebaut, I., Moshous, D., Mornon, J. P., and de Villartay, J. P. (2002) Metallo-beta-lactamase fold within nucleic acids processing enzymes: the beta-CASP family, Nucleic Acids Res. 30, 3592-3601.
13. Schilling, O., Wenzel, N., Naylor, M., Vogel, A., Crowder, M. W., Makaroff, C. A., and Meyer-Klaucke, W. (2003) Flexible metal binding of the metallo-β-lactamase domain: glyoxalase II incorporates iron, mangananese, and zinc in vivo, Biochemistry 42, 11777-11786.
14. Frazao, C., Suva, G., Gomes, C. M., Matias, P., Coelho, R., Sieker, L., Macedo, S., Liu, M. Y., Oliveira, S., Teixeira, M., Xavier, A. V., Rodrigues-Pousada, C., Carrondo, M. A., and Le Gall, J. (2000) Structure of a dioxygen reduction enzyme from desulfovibrio gigas, Nat. Struct. Biol. 7, 1041-1045.
15. Concha, N. O., Rasmussen, B. A., Bush, K., and Herzberg, O. (1996) Crystal structure of the wide-spectrum binuclear zinc beta-lactamase from Bacteroides fragilis, Structure 4, 823-836.
16. Ullah, J. H., Walsh, T. R., Taylor, I. A., Emery, D. C., Verma, C. S., Gamblin, S. J., and Spencer, J. (1998) The crystal structure of the L1 metallo-beta-lactamase from Stenotrophomonas maltophilia at 1.7 angstrom resolution, J. Mol. Biol. 284, 125-136.
17. Melino, S., Capo, C., Dragani, B., Aceto, A., and Petruzzelli, R. (1998) A zinc-binding motif conserved in glyoxalase II, beta-lactamase and arylsulfatases, Trends Biochem. Sci. 23, 381-382.
18. Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Res. 22, 4673-4680.
19. Turchin, A., and Lawler, J. F., Jr. (1999) The primer generator: a program that facilitates the selection of oligonucleotides for site-directed mutagenesis, Biotechniques 26, 612-676.
20. Segel, I. H. (1993) Enzyme Kinetics, Wiley Classics Library Edition, John Wiley & Sons, New York.
21. Pettifer, R. F., and Hermes, C. (1985) Absolute energy calibration of X-ray radiation from synchrotron sources, J. Appl. Crystallogr. 18, 404-412.
22. Binsted, N., Strange, R. W., and Hasnain, S. S. (1992) Constrained and restrained refinement in EXAFS data analysis with curved wave theory, Biochemistry 31, 12117-12125.
23. Feiters, M. C., Eijkelenboom, A. P., Molting, H. F., Krebs, B., Van Den Ent, F. M., Plasterk, R. H., Kaptein, R., and Boelens, R. (2003) X-ray absorption spectroscopic studies of zinc in the N-terminal domain of HIV-2 integrase and model compounds, J. Synchrotron Radiat. 10, 86-95.
24. de Seny, D., Heinz, U., Wommer, S., Kiefer, M., Meyer-Klaucke, W., Galleni, M., Frère, J. M., Bauer, R., and Adolph, H. W. (2001) Metal ion binding and coordination geometry for wild type and mutants of metallo-beta-lactamase from Bacillus cereus 569/H/9 (BcII): a combined thermodynamic, kinetic, and spectroscopic approach, J. Biol. Chem. 276, 45065-45078.
25. Harding, M. M. (1999) The geometry of metal-ligand interactions relevant to proteins, Acta Cryslallogr. D 55, 1432-1443.
26. Harding, M. M. (2001) Geometry of metal-ligand interactions in proteins, Acta Crystallogr. D 57, 401-411.
27. Mijovilovich, A., and Meyer-Klaucke, W. (2001) Determination of metal-metal distances: significance and accuracy, J. Synchrotron Radiat. 8, 692-694.
28. Riggs-Gelasco, P. J., Stemmler, T. L., and Penner-Hahn, J. E. (1995) XAFS of dinuclear metal sites in proteins and model compounds, Coord. Chem. Rev. 144, 245-286.
29. Lin, Y., Dotsch, V., Wintner, T., Peariso, K., Myers, L. C., Penner-Hahn, J. E., Verdine, G. L., and Wagner, G. (2001) Structural basis for the functional switch of the E. coli Ada protein, Biochemistry 40, 4261-4271.
30. Jacquamet, L., Aberdam, D., Adrait, A., Hazemann, J. L., Latour, J. M., and Michaud-Soret, I. (1998) X-ray absorption spectroscopy of a new zinc site in the fur protein from Escherichia coli, Biochemistry 37, 2564-2571.
31. Peariso, K., Zhou, Z. S., Smith, A. E., Matthews, R. G., and Penner-Hahn, J. E. (2001) Characterization of the zinc sites in cobalamin-independent and cobalamin-dependent methionine synthase using zinc and selenium X-ray absorption spectroscopy, Biochemistry 40, 987-993.
32. Tobin, D. A., Pickett, J. S., Hartman, H. L., Fierke, C. A., and Penner-Hahn, J. E. (2003) Structural characterization of the zinc site in protein farnesyltransferase, J. Am. Chem. Soc. 125, 9962-9969.
33. Mijovilovich, A., and Meyer-Klaucke, W. (2003) Simulating the XANES of metalloenzymes - a case study, J. Synchrotron Radiat. 10, 64-68.
34. Wang, Z., Fast, W., Valentine, A. M., and Benkovic, S. J. (1999) Metallo-beta-lactamase: structure and mechanism, Curr. Opin. Chem. Biol. 3, 614-622.
35. Wang, Z., Fast, W., and Benkovic, S. J. (1999) On the mechanism of the metallo-beta-lactamase from Bacteroides fragilis, Biochemistry 38, 10013-10023.
36. Auld, D. S. (2001) Zinc coordination sphere in biochemical zinc sites, BioMetals 14, 271-313.
37. Yanchak, M. P., Taylor, R. A., and Crowder, M. W. (2000) Mutational analysis of metallo-beta-lactamase CcrA from Bacteroides fragilis, Biochemistry 39, 11330-11339.
38. Crowder, M. W., Wang, Z., Franklin, S. L., Zovinka, E. P., and Benkovic, S. J. (1996) Characterization of the metal-binding sites of the beta-lactamase from Bacteroides fragilis, Biochemistry 35, 12126-12132.
39. de Seny, D., Prosperi-Meys, C., Bebrone, C., Rossolini, G. M., Page, M. I., Noel, P., Frère, J. M., and Galleni, M. (2002) Mutational analysis of the two zinc-binding sites of the Bacillus cereus 569/H/9 metallo-beta- lactamase, Biochem. J. 363, 687-696.
40. Eggers-Borkenstein, P., Priggemeyer, S., Krebs, B., Henkel, G., Simonis, U., Pettifer, R. F., Nolting, H. F., and Hermes, C. (1989) Extended X-ray absorption fine structure (EXAFS) investigations of model compounds for zinc enzymes, Eur. J. Biochem. 186, 667-675.