EPR and X-ray crystallographic characterization of the product-bound form of the MNII-loaded methionyl aminopeptidase from Pyrococcus furiosus

Biochemistry

Volumn 44, Issue 1, 2005, Pages 121-129

  Copik, Alicja J ^a   Nocek, Boguslaw P ^b   Swierczek, Sabina I ^a   Ruebush, Shane ^a   Se, Bok Jang ^b   Meng, Lu ^a   D'Souza, Ventris M ^a   Peters, John W ^b   Bennett, Brian ^c   Holz, Richard C ^a  

^a UTAH STATE UNIVERSITY   (United States)

^b MONTANA STATE UNIVERSITY   (United States)

^c MEDICAL COLLEGE OF WISCONSIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CRYSTAL STRUCTURE; ELECTRON SPIN RESONANCE SPECTROSCOPY; IONS; MOLECULES; WATER; X RAY CRYSTALLOGRAPHY;

BINDING MODE; HYPERFINE SPLIT PATTERN; INTENSE SIGNALS; METALLOACTIVE SITES;

ENZYMES;

AMINE; CARBOXYLIC ACID; MANGANESE; METHIONINE; METHIONYL AMINOPEPTIDASE;

ARTICLE; CRYSTAL STRUCTURE; ELECTRON SPIN RESONANCE; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL; PYROCOCCUS FURIOSUS; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY;

AMINOPEPTIDASES; CRYSTALLOGRAPHY, X-RAY; ELECTRON SPIN RESONANCE SPECTROSCOPY; ESCHERICHIA COLI; MANGANESE; PROTEIN CONFORMATION; PYROCOCCUS FURIOSUS;

ESCHERICHIA COLI; PYROCOCCUS; PYROCOCCUS FURIOSUS;

EID: 19944427515     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi048123+     Document Type: Article

References (48)

1. α-Acetyl Transferase Families, Trends Biochem. Sci. 23, 263.
2. Bradshaw, R. A. (1989) Protein Translocation and Turnover in Eukaryotic Cells, Trends Biochem. Sci. 14, 276.
3. Arfin, S. M., and Bradshaw, R. A. (1988) Cotranslational Processing and Protein Turnover in Eukaryotic Cells. Biochemistry 27, 7979.
4. Hirel, P.-H., Schmitter, J.-M., Dessen, P., Fayat, G., and Blanquet, S. (1989) Extent of N-Terminal Methionine Excision from Escherichia coli Proteins Is Goverened by the Side-Chain Length of the Penultimate Amino Acid. Proc. Natl. Acad. Sci. U.S.A. 86, 8247.
5. Meinnel, T., Mechulam, Y., and Blanquet, S. (1993) Methionine as Translation Start Signal - A Review of the Enzymes of the Pathway in Escherichia coli, Biochimie 75, 1061.
6. Chang, S.-Y. P., McGary, E. C., and Chang, S. (1989) Methionine Aminopeptidase Gene of Escherichia coli Is Essential for Cell Growth, J. Bacteriol 171, 4071.
7. Li, X., and Chang, Y.-H. (1995) Amino-Terminal Protein Processing in Saccharomyces cerevisiae Is an Essential Function That Requires Two Distinct Methionine Aminopeptidases, Proc. Natl. Acad. Sci. U.S.A. 92, 12357.
8. Miller, C. G., Kukral, A. M., Miller, J. L., and Movva, N. R. (1989) Pepm Is an Essential Gene in Salmonella typhimurium, J. Bacteriol. 171, 5215.
9. Griffith, E. C., Su, Z., Turk, B. E., Chen, S., Chang, Y.-H., Wu, Z., Biemann, K., and Liu, J. O. (1997) Methionine Aminopeptidase (Type 2) Is the Common Target for Angiogenesis Inhibitors Agm-1470 and Ovalicin, Chem. Biol. 4, 461.
10. Sin, N., Meng, L., Wang, M. Q., Wen, J. J., Bornmann, W. G., and Crews, C. M. (1997) The Anti-Angiogenic Agent Fumagillin Covalently Binds and Inhibits the Mathionine Aminopeptidase, Metap-2, Proc. Natl. Acad. Sci. U.S.A. 94, 6099.
11. Arfin, S. M., Kendall, R. L., Hall, L., Weaver, L. H., Stewart, A. E., Matthews, B. W., and Bradshaw, R. A. (1995) Eukaryotic Methionyl Aminopeptidases: Two Classes of Cobalt-Dependent Enzymes, Proc. Natl. Acad. Sci. U.S.A. 92, 7714.
12. Tahirov, T. H., Oki, H., Tsukihara, T., Ogasahara, K., Yutani, K., Ogata, K., Izu, Y., Tsunasawa, S., and Kato, I. (1998) Crystal Structure of the Methionine Aminopeptidase from the Hyperthermophile, Pyrococcus Furiosus, J. Mol. Biol. 284, 101.
13. Lowther, W. T., Orville, A. M., Madden, D. T., Lim, S., Rich, D. H., and Matthews, B. W. (1999) Escherichia coli Methionine Aminopeptidase: Implications of Crystallographic Analyses of the Native, Mutant, and Inhibited Enzymes for the Mechanism of Catalysis, Biochemistry 38, 7678.
14. Roderick, L. S., and Matthews, B. W. (1993) Structure of the Cobalt-Dependent Methionine Aminopeptidase from Escherichia coli: A New Type of Proteolytic Enzyme, Biochemistry 32, 3907.
15. Liu, S., Widom, J., Kemp, C. W., Crews, C. M., and Clardy, J. (1998) Structure of the Human Methionine Aminopeptidase-2 Complexed with Fumagillin, Science 282, 1324.
16. Oefner, C., Douangamath, A., D'Arcy, A., Hafeli, S., Mareque, D., MacSweeney, A., Padilla, L. Pierau, S., Schulz, H., Thormann, M., Wadman, S., and Dale, G. E. (2003) The 1.15 Å Crystal Structure of the Staphylococcus aureus Methionyl-Aminopeptidase and Complexes with Triazole-Based Inhibitors. J. Mol. Biol. 332, 13.
17. II as a Cofactor: A Case of Mistaken Identity, Protein Sci. 7, 2684.
18. D'souza, V. M., and Holz, R. C. (1999) The Methionyl Aminopeptidase from Escherichia coli Is an Iron(II) Containing Enzyme, Biochemistry 38, 11079.
19. D'souza, V. M., Bennett, B., Copik, A. J., and Holz, R. C. (2000) Characterization of the Divalent Metal Binding Properties of the Methionyl Aminopeptidase from Escherichia coli, Biochemistry 39, 3817.
20. Meng, L., Ruebush, S., D'souza, V. M., Copik, A. J., Tsunasawa, S., and Holz, R. C. (2002) Overexpression and Divalent Metal Binding Studies for the Methionyl Aminopeptidase from Pyrococcus furiosus. Biochemistry 41, 7199.
21. Cosper, N. J., D'souza, V., Scott, R., and Holz, R. C. (2001) Structural Evidence That the Methionyl Aminopeptidase from Escherichia coli Is a Mononuclear Metalloprotease, Biochemistry 40, 13302.
22. Wang, J., Sheppard, G. S., Lou, P., Kawai, M., Park, C., Egan, D. A., Schneider, A., Bouska, J., Lesniewski, R., and Henkin, J. (2003) Physiologically Relevant Metal Cofactor for Methionine Aminopeptidase-2 Is Manganese, Biochemistry 42, 5035.
23. Griffin, M., Muys, A., Noble, C., Wang, D., Eldershaw, C., Gates, K. E., Burrage, K., and Hanson, G. R. (1999) Xsophe, a Computer Simulation Software Suite for the Analysis of Electron Paramagnetic Spectrs, Mol. Phys. Rep. 26, 60.
24. Powell, H. R. (1999) The Rossmann Fourier Autoindexing Algorithm in Mosflm, Acta Crystallogr., Sect. D 55, 1690.
25. Collaborative Computational Project, No. 4 (1994) Acta Crystallogr., Sect. D 50, 760-763.
26. Navaza, J. (2001) Implementation of Molecular Replacement in Amore, Acta Crystallogr., Sect. D 57, 1367.
27. Oldfield, T. J. (2001) X-Ligand: An Application for the Automated Addition of Flexible Ligands into Electron Density. Acta Crystallogr., Sect. D 57, 696.
28. Jones, T. A., Zou, J.-Y., Cowan, S. W., and Kjeldgaard, M. (1991) Improved Methods for the Building of Protein Models in Electron Density Maps and the Location of Errors in These Models. Acta Crystallogr., Sect. A 47, 110.
29. Brunger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, J. S., Jiang, J., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren. G. L. (1998) Crystallography and NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr., Sect. D 54, 905-921.
30. Laskowski, R. A., Moss, D. S., and Thornton, J. M. (1993) Main-Chain Bond Lengths and Bond Angles in Protein Structures, J. Mol. Biol. 231, 1049.
31. II-Loaded Methionyl Aminopeptidase from Escherichia coli, J. Eur. Biochem., manuscript submitted.
32. Reed, G. H., and Markham, G. D. (1984) Biol. Magn. Reson. 6, 73.
33. Griscom, D. L., and Griscom, R. E. (1967) J. Chem. Phys. 47, 2711.
34. Schreurs, J. W. H. (1978) J. Chem. Phys. 69, 2151.
35. Whiting, A. K., Boldt, Y. R., Hendrich, M. P., Wackett, L. P., and Que, L. (1996) Manganese(II)-Dependent Extradiol-Cleaving Chatechol Dioxygenase from Arthrobacter globiformis Cm-2, Biochemistry 35, 160.
36. 2+ Is a Native Metal Ion Activator for Bacteriophage λ Protein Phosphatase, Biochemistry 41, 15404.
37. 2 Cluster, Biochemistry 38, 6943.
38. II Centers in Rat Liver Arginase, J. Am. Chem. Soc. 114, 10992.
39. Golombek, A. P., and Hendrich, M. P. (2003) Quantitative Analysis of Dinuclear Manganese(II) EPR Spectra, J. Magn. Reson. 165, 33.
40. Khangulov, S. V., Pessiki, P. J., Barynin, V. V., Ash, D. E., and Dismukes, G. C. (1995) Determination of the Metal Ion Separation and Energies of the Three Lowest Electronic States of Dimanganese(II, II) Complexes and Enzymes: Catalase and Liver Arginase, Biochemistry 34, 2015.
41. Khangulov, S. V., Sossong, T. M. J., Ash, D. E., and Dismukes, G. C. (1998) L-Arginine Binding to Liver Arginase Requires Proton Transfer to Gateway Residue His141 and Coordination of the Guanidinium Group to the Dimanganese(II, II) Center, Biochemistry 37, 8539.
42. D'souza, V. M., Swierczek, S. I., Cosper, N. J., Meng, L., Ruebush, S., Copik, A. J., Scott, R. A., and Holz, R. C. (2002) Kinetic and Structural Characterization of Manganese(II)-Loaded Methionyl Aminopeptidases, Biochemistry 41, 13096.
43. Cottrell, G., Hooper, N. M., and Turner, A. J. (2000) Cloning, Expression, and Characterization of the Human Cytosolic Aminopeptidase: A Single Manganese(II)-Dependent Enzyme, Biochemistry 39, 15121.
44. II EPR Spectra Using a Full Spin-Hamiltonian Approach." (1996) J. Magn. Reson. B. 111, 127.
45. Lowther, T. W., Zhang, Y., Sampson, P. B., Honek, J. F., and Matthews, B. W. (1999) Insights into the Mechanism of E. coli Methionine Aminopeptidase from the Structural Analysis of Reaction Products and Phosphorous-Based Transition State Analogs, Biochemistry 38, 14810.
46. Ustynyuk, L., Bennett, B., Edwards, T., and Holz, R. C. (1999) Inhibition of the Aminopeptidase from Aeromonas proteolytica by Aliphatic Alcholols. Characterization of the Hydrophobic Substrate Recognition Site, Biochemistry 38, 11433.
47. Stamper, C., Bienvenue, D., Moulin, A., Bennett, B., Ringe, D., Petsko, G., and Holz, R. C. (2004) Spectroscopic and X-ray Crystallographic Characterization of the Bestatin-Bound Form of the Aminopeptidase from Aeromonas proteolytica, Biochemistry 43, 9620.
48. Copik, A. J., Swierczek, S. I., Lowther, W. T., D'souza, V., Matthews, B. W., and Holz, R. C. (2003) Kinetic and Spectroscopic Characterization of the H178a Mutant of the Methionyl Aminopeptidase from Escherichia coli, Biochemistry 42, 6283.