A Conformational Mimic of the MgATP-Bound "On State" of the Nitrogenase Iron Protein

Biochemistry

Volumn 43, Issue 7, 2004, Pages 1787-1797

  Sen, Sanchayita ^a   Igarashi, Robert ^b   Smith, Archer ^c   Johnson, Michael K ^c   Seefeldt, Lance C ^b   Peters, John W ^a  

^a MONTANA STATE UNIVERSITY   (United States)

^b UTAH STATE UNIVERSITY   (United States)

^c UNIVERSITY OF GEORGIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONS; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; ELECTRON SPIN RESONANCE SPECTROSCOPY; LIGHT ABSORPTION; RAMAN SPECTROSCOPY; ULTRAVIOLET RADIATION;

RATIONALIZATION; RIGID-BODY REORIENTATION;

PROTEINS;

ADENOSINE TRIPHOSPHATE MAGNESIUM; IRON; NITROGENASE;

AMINO ACID SEQUENCE; ARTICLE; AZOTOBACTER VINELANDII; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; ELECTRON SPIN RESONANCE; ENZYME CONFORMATION; METAL BINDING; NONHUMAN; PRIORITY JOURNAL; RAMAN SPECTROMETRY;

ADENOSINE TRIPHOSPHATE; AZOTOBACTER VINELANDII; BACTERIAL PROTEINS; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; IRON-SULFUR PROTEINS; LEUCINE; MODELS, MOLECULAR; MOLECULAR MIMICRY; MOLYBDOFERREDOXIN; MUTAGENESIS, SITE-DIRECTED; OXIDOREDUCTASES; PROTEIN BINDING; PROTEIN CONFORMATION; SPECTROPHOTOMETRY, ULTRAVIOLET; SPECTRUM ANALYSIS, RAMAN;

AZOTOBACTER VINELANDII;

EID: 1242352960     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi0358465     Document Type: Article

References (67)

1. Howard, J. B., and Rees, D. C. (1994) Nitrogenase: A nucleotide-dependent molecular switch, Annu. Rev. Biochem. 63, 235-264.
2. Rees, D. C., and Howard, J. B. (2000) Nitrogenase: standing at the crossroads, Curr. Opin. Chem. Biol. 4, 559-566.
3. Seefeldt, L. C., and Dean, D. R. (1997) Role of nucleotides in nitrogenase catalysis, Acc. Chem. Res. 30, 260-266.
4. Koonin, E. V. (1993) A superfamily of ATPases with diverse functions containing either classical or deviant ATP-binding motifs, J. Mol. Biol. 229, 1165-1174.
5. Schulz, G. E. (1992) Binding of nucleotides by proteins, Curr. Opin. Struct. Biol. 2, 61-67.
6. Sprang, S. R. (1997) G protein mechanisms: Insights from structural analysis, Annu. Rev. Biochem. 66, 639-678.
7. Sunahara, R. K., Tesmer, J. J., Gilman, A. G., and Sprang, S. R. (1997) Crystal structure of the adenylate cyclase activiator Gsγ, Science 278, 1943-1947.
8. -, Nature 372, 276-279.
9. Kjeldgaard, M., and Nyborg, J. (1992) Refined structure of elongation factor EF-Tu from Escherichia coli, J. Mol. Biol. 223, 721-742.
10. Jurnak, F. (1985) Structure of the GDP domain of EF-Tu and location of the amino acids homologous to ras oncogene proteins, Science 230, 32-36.
11. Story, R. M., and Steitz, T. A. (1992) Structure of the recA protein-ADP complex, Nature 355, 374-376.
12. Story, R. M., Weber, I. T., and Steitz, T. A. (1992) The structure of the E. coli recA protein monomer and polymer, Nature 355, 318-325.
13. Rayment, I. (1996) The structural basis of the myosin ATPase activity, J. Biol. Chem. 271, 15850-15853.
14. Rayment, I., and Holden, H. M. (1994) The three-dimensional structure of a molecular motor, Trends Biochem. Sci. 19, 129-134.
15. Rayment, I., Holden, H. M., Whittaker, M., Yohn, C. B., Lorenz, M., Holmes, K. C., and Milligan, R. A. (1993) Structure of the actin-myosin complex and its implication for muscle contraction, Science 261, 58-65.
16. Rayment, I., Rypniewski, W. R., Schmidt-Base, K., Smith, R., Tomchick, D. R., Benning, M. M., Winkelmann, D. A., Wesenberg, G., and Holden, H. M. (1993) Three-dimensional structure of myosin subfragment-1: a molecular motor, Science 261, 50-58.
17. Robson, R. L. (1984) Identification of possible adenine nucleotide-binding sites in nitrogenase Fe- and MoFe-proteins by amino acid sequence comparison, FEBS Lett. 173, 394-398.
18. Bolin, J. T., Ronco, A. E., Morgan, T. V., Mortenson, L. E., and Xuong, N. (1993) The unusual metal clusters of nitrogenase: structural features revealed by X-ray anomalous diffraction studies of the MoFe protein from Clostridium pasteurianum, Proc. Natl. Acad. Sci. U.S.A. 90, 1078-1082.
19. Chan, M. K., Kim, J., and Rees, D. C. (1993) The nitrogenase FeMo-cofactor and P-cluster pair: 2.2 Å resolution structures, Science 260, 792-794.
20. Georgiadis, M. M., Komiya, H., Chakrabarti, P., Woo, D., Kornuc, J. J., and Rees, D. C. (1992) Crystallographic structure of the nitrogenase iron protein from Azotobacter vinelandii, Science 257, 1653-1659.
21. Kim, J., and Rees, D. C. (1992) Crystallographic structure and functional implications of the nitrogenase molybdenum iron protein from Azotobacter vinelandi, Nature 360, 553-560.
22. Kim, J., and Rees, D. C. (1992) Structural models for the metal centers in the nitrogenase molybdenum-iron protein, Science 257, 1677-1682.
23. Kim, J., Woo, D., and Rees, D. C. (1993) X-ray crystal structure of the nitrogenase molybdenum-iron protein from Clostridium pasteurianum at 3. 0-Å resolution, Biochemistry 32, 7104-7015.
24. Mayer, S. M., Lawson, D. M., Gormal, C. A., Roe, S. M., and Smith, B. E. (1999) New insights into structure-function relationships in nitrogenase: A 1.6 angstrom resolution X-ray crystallographic study of Klebsiella pneumoniae MoFe-protein, J. Mol. Biol. 292, 871-891.
25. Peters, J. W., Stowell, M. H., Soltis, S. M., Finnegan, M. G., Johnson, M. K., and Rees, D. C. (1997) Redox-dependent structural changes in the nitrogenase P-cluster, Biochemistry 36, 1181-1187.
26. Jang, S. B., Seefeldt, L. C., and Peters, J. W. (2000) Insights into nucleotide signal transduction in nitrogenase: structure of an iron protein with MgADP bound, Biochemistry 39, 14745-14752.
27. --stabilized nitrogenase complex and its implications for signal transduction, Nature 387, 370-376.
28. 4-stabilized structure, Biochemistry 41, 15557-15565.
29. 4, Biochemistry 34, 8960-8972.
30. Gulick, A. M., Bauer, C. B., Thoden, J. B., Pate, E., Yount, R. G., and Rayment, I. (2000) X-ray structures of the Dictyostelium discoideum myosin motor domain with six non-nucleotide analogs, J. Biol. Chem. 275, 398-408.
31. Lanzilotta, W. N., Fisher, K., and Seefeldt, L. C. (1996) Evidence for electron transfer from the nitrogenase iron protein to the molybdenum-iron protein without MgATP hydrolysis: Characterization of a tight protein-protein complex, Biochemistry 35, 7188-7196.
32. Ryle, M. J., and Seefeldt, L. C. (1996) Elucidation of MgATP signal transduction pathway in the nitrogenase iron protein: formation of a conformation resembling the MgATP-bound state by protein engineering, Biochemistry 35, 4766-4775.
33. Chiu, H., Peters, J. W., Lanzilotta, W. N., Ryle, M. J., Seefeldt, L. C., Howard, J. B., and Rees, D. C. (2001) MgATP-bound and nucleotide-free structures of a nitrogenase protein complex between the Leu 127 Δ-Fe-protein and the MoFe-protein, Biochemistry 40, 641-650.
34. Cudney, B., Patel, S., Weisgraber, K., and Newhouse, Y. (1994) Screening and optimization strategies for macromolecular crystal growth, Acta Crystallogr., Sect. D: Biol. Crystallogr. 50, 4114-4123.
35. Jancarik, J., and Kim, S. H. (1991) Sparse matrix sampling: a screening method for crystallization of proteins, J. Appl. Crystallogr. 24, 409-411.
36. Leslie, A. G. W. (1992) Recent changes to the MOSFLM package for processing film and imaging plate data, in Joint CCP4 and ESF-EACBM newsletter on protein crystallography.
37. Collaborative Computational Project (1994) The CCP4 suite: programs for protein crystallography, Acta Crystallogr. D50, 760-763.
38. Navaza, J. (1994) AMORE - an automated package for molecular replacement, Acta Crystallogr. A50, 157-163.
39. Hendrickson, W. A. (1991) Determination of macromolecular structures from anomalous diffraction of synchrotron radiation, Science 254, 51-58.
40. Terwilliger, T. C., and Berendzen, J. (1999) Automated structure solution of MIR and MAD, Acta Crystallogr., Sect. D: Biol. Crystallogr. 55, 849-861.
41. Matthews, B. W. (1968) Solvent content of protein crystals, J. Mol. Biol. 33, 491-497.
42. Peters, J. W., and Bellamy, H. D. (1999) Extension of Fe MAD phases in the structure determination of a multiple [FeS] cluster containing hydrogenase, J. Appl. Crystallogr. 32, 1180-1182.
43. Lamzin, V. S., and Perrakis, A. (2000) Current state of automated crystallographic data analysis, Nat. Struct. Biol. 7 (Suppl.), 978-981.
44. Lamzin, V. S., Perrakis, A., Bricogne, G., Jiang, J., Swaminathan, S., and Sussman, J. L. (2000) Apotheosis, not apocalypse: methods in protein crystallography, Acta Crystallogr., Sect. D: Biol. Crystallogr. 56, 1510-1511.
45. Jones, T. A., Zou, J. Y., Cowan, S. W., and Kjeldgaard. (1991) Improved methods for building protein models in electron density maps and the location of errors in these models, Acta Crystallogr. A47, 110-119.
46. Brunger, A. T., Kuriyan, J., and Karplus, M. (1987) Crystallographic R factor refinement by molecular dynamics, Science 235, 458-460.
47. Brunger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination, Acta Crystallogr., Sect. D: Biol. Crystallogr. 54, 905-921.
48. Drozdzewski, P. M., and Johnson, M. K. (1988) A simple anaerobic cell for low temperature Raman spectroscopy, Appl. Spectrosc. 42, 1575-1577.
49. Hauptman, H. (1997) Phasing methods for protein crystallography, Curr. Opin. Struct. Biol. 7, 672-680.
50. Schlessman, J. L., Woo, D., Joshua-Tor, L., Howard, J. B., and Rees, D. C. (1998) Conformational variability in structures of the nitrogenase iron proteins from Azotobacter vinelandii and Clostridium pasteurianum, J. Mol. Biol. 280, 669-685.
51. Molloy, J. E., and Veigel, C. (2003) Biophysics. Myosin motors walk the walk, Science 300, 2045-2046.
52. Yildiz, A., Forkey, J. N., McKinney, S. A., Ha, T., Goldman, Y. E., and Selvin, P. R. (2003) Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization, Science 300, 2061-2065.
53. Phe residues in Azotobacter vinelandii MoFe protein-Fe protein interaction, J. Inorg. Biochem. 80, 195-204.
54. Anderson, G. L., and Howard, J. B. (1984) Reactions with oxidized iron protein of Azotobacter vinelandii nitrogenase: formation of a 2Fe center, Biochemistry 23, 2118-2122.
55. Lindahl, P. A., Gorelick, N. J., Münck, E., and Orme-Johnson, W. H. (1987) EPR and Mössbauer studies of nucleotide-bound nitrogenase iron protein from Azotobacter vinelandii, J. Biol. Chem. 262, 14945-14953,
56. Fu, W., Morgan, T. V., Mortenson, L. E., and Johnson, M. K. (1991) Resonance Raman studies of the [4Fe-4S] to [2Fe-2S] cluster conversion in the iron protein of nitrogenase, FEBS Lett. 284, 165-168.
57. Spiro, T. G., Czernuszewicz, R. S., and Han, S. (1988) Iron-sulfur proteins and analogue complexes, in Resonance Raman spectra of heme and metalloproteins (Spiro, T. G., Ed.) pp 523-554, John Wiley & Sons, New York.
58. Fu, W., Drozdzewski, P. M., Adams, M. W. W., Morgan, T. V., Mortenson, L. E., LeGall, J., Peck, H. D., Jr., DerVartanian, D. V., and Johnson, M. K. (1993) Resonance Raman studies of iron-only hydrogenases, Biochemistry 32, 4813-4819.
59. 2 protein resonance Raman spectra revisited: structural variations among adrenodoxin, ferredoxin, and red paramagnetic protein, J. Am. Chem. Soc. 111, 3505-3511.
60. Fu, W., Drozdzewski, P. M., Davies, M. D., Sligar, S. G., and Johnson, M. K. (1992) Resonance Raman and magnetic circular dichroism studies of reduced [2Fe-2S] proteins, J. Biol. Chem. 267, 15502-15510.
61. + clusters in Spectroscopic Methods in Bioinorganic Chemistry (Solomon, E. I., and Hodgson, K. O., Eds.) pp 286-301, American Chemical Society, Washington, DC.
62. Broderick, J. B., Duderstadt, R. E., Fernandez, D. C., Wojtuszewski, K., Henshaw, T. F., and Johnson, M. K. (1997) Pyruvate formate-lyase activating enzyme is an iron-sulfur protein, J. Am. Chem. Soc. 119, 7396-7397.
63. Johnson, M. K., Staples, C. R., Duin, E. C., Lafferty, M. E., and Duderstadt, R. E. (1998) Novel roles for Fe-S clusters in stabilizing or generating radical intermediates, Pure Appl. Chem. 70, 939-946.
64. Pierrel, F., Hernandez, H., Johnson, M. K., Fontecave, M., and Atta, M. (2003) MiaB Protein from Thermotoga maritima: characterization of an extremely thermophilic tRNA-methylthiotransferase, J. Biol. Chem. 278, 29515-29524.
65. Agar, J. N., Krebs, B., Frazzon, J., Huynh, B. H., Dean, D. R., and Johnson, M. K. (2000) IscU as a scaffold for iron-sulfur cluster biosynthesis: sequential assembly of [2Fe-2S] and [4Fe-4S] clusters in IscU, Biochemistry 39, 7856-7862.
66. Krebs, C., Agar, J. N., Smith, A. D., Frazzon, J., Dean, D. R., Huynh, B. H., and Johnson, M. K. (2001) IscA, an alternate scaffold for Fe-S cluster biosynthesis, Biochemistry 40, 14069-14080.
67. Agar, J. N., Dean, D. R., and Johnson, M. K. (2003) Iron-sulfur cluster biosynthesis, in Biochemistry and Physiology of Anaerobic Bacteria (Ljungdahl, L. G., Adams, M. W. W., Barton, L. L., Ferry, J. G., and Johnson, M. K., Eds.) pp 46-66, Springer-Verlag, New York.