Determination of the structure of oxidised Desulfovibrio africanus ferredoxin I by 1H NMR spectroscopy and comparison of its solution structure with its crystal structure

Journal of Molecular Biology

Volumn 277, Issue 3, 1998, Pages 683-706

  Davy, Sharon L ^a   Osborne, Michael J ^a   Moore, Geoffrey R ^a  

^a Ctr Metalloprotein Spectrosc B   (United Kingdom)

Author keywords

Fe4S4 centres; Ferredoxin; NMR; Structure; X ray

Indexed keywords

FERREDOXIN;

ARTICLE; COMPUTER PROGRAM; COVALENT BOND; CRYSTAL STRUCTURE; DESULFOVIBRIO; HYDROGEN BOND; NONHUMAN; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; X RAY ANALYSIS;

BACTERIA (MICROORGANISMS); DESULFOVIBRIO; DESULFOVIBRIO AFRICANUS; NEGIBACTERIA;

EID: 0032478518     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1631     Document Type: Article

References (76)

1. Adman E.T., Sieker L.C., Jensen L.H. Structure of a bacterial ferredoxin. J. Biol. Chem. 248:1973;3987-3996
2. Adman E.T., Sieker L.C., Jensen L.H. Structure of Peptococcus aerogenes ferredoxin. Refinement at 2 Å resolution. J. Biol. Chem. 251:1976;3801-3806
3. Armstrong F.A., Butt J.N., George S.J., Hatchikian E.C., Thomson A.J. Evidence for reversible multiple redox transformations of [3Fe-4S] clusters. FEBS Letters. 259:1989;15-18
4. 4clusters in ferredoxins and high-potential iron proteins. New information from X-ray crystallography and resonance Raman spectroscopy. J. Am. Chem. Soc. 113:1991;2055-2064
5. Banci L., Bertini I., Luchinat C. Two-dimensional nuclear magnetic resonance spectra of paramagnetic systems. Methods Enzymol. 239:1994;485-514
6. Banci L., Bertini I., Eltis L.D., Felli I.C., Kastrau D.H.W., Luchinat C., Piccioli M., Pierattelli R., Smith M. The three-dimensional structure in solution of the paramagnetic high-potential iron-sulphur protein I fromEctothiorhodospira halophila through nuclear magnetic resonance. Eur. J. Biochem. 225:1994;715-725
7. Banci L., Bertini I., Dikiy A., Kastrau D.H.W., Luchinat C., Sompornpisut P. The three-dimensional solution structure of the reduced high-potential iron-sulphur protein from Chromatium vinosum through NMR. Biochemistry. 34:1995;206-219
8. 2] ferredoxin in solution. Biochemistry. 35:1996;12831-12841
9. Bax A., Davis D.G. MLEV-17-based two-dimensional homonuclear magnetization transfer spectroscopy. J. Magn. Reson. 65:1985;355-360
10. Bax A., Davis D.G., Sarkar S.K. An improved method for two-dimensional heteronuclear relayed coherence transfer NMR spectroscopy. J. Magn. Reson. 63:1985;230-234
11. Beinert H., Holm R.H., Munck E. Iron-sulfur clusters Nature's modular, multipurpose structures. Science. 277:1997;653-659
12. Bentrop D., Bertini I., Capozzi F., Dikiy A., Eltis L., Luchinat C. Three-dimensional structure of the reduced C77S mutant of the Chromatium vinosum high-potential iron-sulphur protein through nuclear magnetic resonance comparison with the solution structure of the wild-type protein. Biochemistry. 35:1996;5928-5936
13. 4] ferredoxin from Clostridium pasteurianum. FEBS Letters. 289:1991;253-256
14. 4centers in ferredoxins studied through proton and carbon hyperfine coupling. Sequence-specific assignments of cysteines in ferredoxins from Clostridium acidi urici and Clostridium pasteurianum. J. Am. Chem. Soc. 116:1994;651-660
15. Bertini I., Donaire A., Feinberg B.A., Luchinat C., Piccioli M., Yuan H. Solution structure of the oxidized 2[4Fe-4S] ferredoxin from Clostridium pasteurianum. Eur. J. Biochem. 232:1995;192-205
16. Bertini I., Dikiy A., Kastrau D.H.W., Luchinat C., Sompornpisut P. Three-dimensional solution structure of the oxidized high potential iron-sulphur protein from Chromatium vinosum through NMR. Comparative analysis with the solution structure of the reduced species. Biochemistry. 34:1995;9851-9858
17. Bertini I., Felli I.C., Luchinat C., Rosata A. A complete relaxation matrix refinement of the solution structure of a paramagnetic metalloprotein reduced HiPIP I fromEctothiorhodospira halophila. Proteins: Struct. Funct. Genet. 24:1996;158-164
18. Bertini I., Couture M.M.J., Donaire A., Eltis L.D., Felli I.C., Luchinat C., Piccioli M., Rosato A. The solution structure refinement of the paramagnetic reduced high-potential iron-sulphur protein I fromEctothiorhodospira halophila by using isotope labeling and nuclear relaxation. Eur. J. Biochem. 241:1996;440-452
19. Bertini I., Luchinat C., Rosata A. The solution structure of paramagnetic metalloproteins. Prog. Bioph. Mol. Biol. 66:1996;43-80
20. Brünger A.T. X-PLOR version 3.1 a System for X-ray Crystallography and NMR. 1992;Yale University Press, New Haven, CT
21. Bruschi M., Hatchikian E.C. Non-heme iron proteins of Desulfovibrio. The primary structure of ferredoxin I from Desulfovibrio africanus. Biochimie. 64:1982;503-507
22. Butt J.N., Armstrong F.A., Breton J., George S.J., Thomson A.J., Hatchikian E.C. Investigation of metal-ion uptake reactivities of [3Fe-4S] clusters in proteins voltammetry of coadsorbed ferredoxin aminocyclitol films at graphite-electrodes and spectroscopic identification of transformed clusters. J. Am. Chem. Soc. 113:1991;6663-6670
23. 1+centers in a ferredoxin. J. Am. Chem. Soc. 113:1991;8948-8950
24. Cammack R. Iron-sulfur clusters in enzymes themes and variations. Cammack R. Advances in Inorganic Chemistry. vol. 38:1992;281-322 Academic Press Ltd, San Diego, CA
25. Campbell I.D., Dobson C.M., Moore G.R., Perkins S.J., Williams R.J.P. Temperature dependent molecular motion of a tyrosine residue of ferrocytochrome c. FEBS Letters. 70:1976;96-100
26. Carter C.W. Jr, Kraut J., Freer S.T., Alden R.A. Comparison of oxidation-reduction site geometries in oxidised and reduced Chromatium high-potential iron protein and oxidised Peptococcus aerogenes ferredoxin. J. Biol. Chem. 249:1974;6339-6346
27. Cheng H., Markley J.L. NMR spectroscopic studies of paramagnetic proteins iron-sulphur proteins. Annu. Rev. Biophys. Biomol. Struct. 24:1995;209-237
28. Davy S.L. PhD. thesis. 1996;University of East Anglia, Norwich, UK
29. 1H NMR spectroscopic studies of Desulfovibrio africanus ferredoxin I revised amino acid sequence and identification of secondary structure. Biochim. Biophys. Acta. 1209:1994;33-39
30. 1H NMR spectroscopy. FEBS Letters. 363:1995;199-204
31. 1H NMR investigation of the electronic structure of the four-iron ferredoxin from the hyperthermophilic archaeon Thermococcus litoralis. J. Am. Chem. Soc. 116:1994;6841-6849
32. 1H NMR investigation of the secondary structure, tertiary contacts and cluster environment of the four-iron ferredoxin from the hyperthermophilic archaeon Thermococcus litoralis. J. Biomol. NMR. 7:1996;35-47
33. Donohue J. On N-H-S hydrogen bonds. J. Mol. Biol. 45:1969;231-235
34. Duée E.D., Fanchon E., Vicat J., Sieker L.C., Meyer J., Moulis J.-M. Refined crystal structure of the 2[4Fe-4S] ferredoxin from Clostridium acidurici at 1. 84 Å resolution. J. Mol. Biol. 243:1994;683-695
35. Eccles C., Günter P., Billeter M., Wüthrich K. Efficient analysis of protein 2D NMR spectra using the software package EASY. J. Biomol. NMR. 1:1991;111-130
36. Freer S.T., Alden R.A., Carter C.W. Jr, Kraut J. Crystallographic structure refinement of Chromatium high potential iron protein at 2 Å resolution. J. Biol. Chem. 250:1975;46-54
37. Frenkiel T.A. Instrumentation and pulse sequences. Roberts G.C.K. NMR of Macromolecules. 1993;35-70 IRL Press, Oxford
38. Fukuyama K., Nagahara Y., Tsukihara T., Katsube Y., Hase T., Matsubara H. Tertiary structure o f Bacillus thermoproteolyticus[4Fe-4S] ferredoxin evolutionary implications for bacterial ferredoxins. J. Mol. Biol. 199:1988;183-193
39. Fukuyama K., Matsubara H., Tsukihara T., Katsube Y. Structure of [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus refined at 2.3 Å resolution structural comparisons of bacterial ferredoxins. J. Mol. Biol. 210:1989;383-398
40. 1H nuclear magnetic resonance spectra of reduced high potential ferredoxin (HiPIP) from Chromatium vinosum. Biochemistry. 31:1992;5632-5639
41. 1H 2D NMR of oxidized ferredoxins from Clostridium pasteurianum andClostridium acidurici. Magn. Reson. Chem. 31:1993;S27-S33
42. 1H NMR investigation of the paramagnetic cluster environment in Pyrococcus furiosus three-iron ferredoxin sequence-specific assignment of ligated cysteines independent of tertiary structure. Biochemistry. 34:1995;600-610
43. Güntert P. DIANA User's Manual and Instructions. 1995;ETH, Zürich
44. Güntert P., Wüthrich K. Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints. J. Biomol. NMR. 1:1991;447-456
45. Güntert P., Braun W., Wüthrich K. Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA. J. Mol. Biol. 217:1991;517-530
46. Hatanaka H., Tanimura R., Katoh S., Inagaki F. Solution structure of ferredoxin from the thermophilic cyanobacterium Synechococcus elongatus and its thermostability. J. Mol. Biol. 268:1997;922-933
47. Hatchikian C.E., Jones H.E., Bruschi M. Isolation and characterization of a rubredoxin and two ferredoxins from Desulfovibrio africanus. Biochim. Biophys. Acta. 548:1979;471-483
48. Hatchikian E.C., Cammack R., Patil D.S., Robinson A.E., Richards A.J.M., George S., Thomson A.J. Spectroscopic characterization of ferredoxin I and ferredoxin II from Desulfovibrio africanus. Biochim. Biophys. Acta. 784:1984;40-47
49. Hendrickson W.A., Wüthrich K. Editors of Encyclopedia of Macromolecular Structures. 1991-1997;Current Biology Ltd, London, UK
50. 4] proteins. Biochemistry. 35:1996;12705-12711
51. 4] clusters in Peptococcus aerogenes ferredoxin , Azotobacter vinelandii ferredoxin I and Chromatium vinosum high-potential iron protein. Biochemistry. 33:1994;10911-10924
52. Kassner R.J., Yang W. A theoretical model for effects of solvent and protein dielectric on the redox potentials of iron-sulfur clusters. J. Am. Chem. Soc. 99:1977;4351-4355
53. Kissinger C.R., Sieker L.C., Adman E.T., Jensen J.H. Refined crystal structure of ferredoxin II from Desulfovibrio gigas at 1.7 Å J. Mol. Biol. 219:1991;693-715
54. Koradi R., Billeter M., Wuthrich K. MOLMOL a program for display and analysis of macromolecular structures. J. Mol. Graph. 14:1996;51-55
55. Krishnamoorthi R., Markley J.L., Cusanovich M.A., Przysiecki C.T., Meyer T.E. Hydrogen-1 nuclear magnetic resonance investigation of high-potential iron-sulfur proteins from Ectothiorhodospira halophila and Ectothiorhodospira vacuolata a comparitive study of hyperfine-shifted resonances. Biochemistry. 25:1986;60-65
56. Laskowski R.A., MacArthur M.W., Moss D.S., Thornton J.M. PROCHECK a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26:1993;283-291
57. Laskowski R.A., Rullmann J.A.C., MacArthur M.W., Kaptein R., Thornton J.M. AQUA and PROCHECK-NMR programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR. 8:1996;477-485
58. Macedo-Ribeiro S., Darimont B., Strener R., Huber R. Small structural changes account for the high thermostability of 1[4Fe-4S] ferredoxin from the hyperthermophilic bacterium. Thermotoga maritima. Structure. 4:1996;1291-1301
59. 1H spin-spin coupling constants in proteins. Biochem. Biophys. Res. Commun. 113:1983;967-974
60. Marion D., Ikura M., Tschudin R., Bax A. Rapid recording of 2D NMR spectra without phase cycling. Application to the study of hydrogen exchange in proteins. J. Magn. Reson. 85:1989;393-399
61. Matsubara H., Saeki K. Structural and functional diversity of ferredoxins and related proteins. Adv. Inorg. Chem. 38:1992;223-280
62. Mouesca J.-M., Chen J.L., Noodleman L., Bashford D., Case D.A. Density functional/ Poisson-Boltzmann calculations of redox potentials for iron-sulfur clusters. J. Am. Chem. Soc. 116:1994;11898-11914
63. Nettisheim D.G., Harder S.R., Feinberg B.A., Otvos J.D. Sequential resonance assignments of oxidised high potential iron-sulfur protein from Chromatium vinosum. Biochemistry. 31:1992;1234-1244
64. Orme-Johnson N.R., Mins W.B., Orme-Johnson W.H., Bartsch R.G., Cusanovich M.A., Peisach J. Oxidation state dependence of proton exchange near the iron-sulfur centers in ferredoxins and high-potential iron-sulfur proteins. Biochim. Biophys. Acta. 748:1983;68-72
65. Osborne M.J., Crowe D., Davy S.L., MacDonald C., Moore G.R. NMR of paramagnetic proteins. Reid D.G. Methods in Molecular Biology. vol. 60:1997;233-269 Humana Press Inc, Totowa. N269
66. Pochapsky T.C., Ye X.M., Ratnaswamy G., Lyons T.A. An NMR-derived model for the solution structure of oxidized putidaredoxin, a 2-Fe, 2-S ferredoxin fromPseudomonas. Biochemistry. 33:1994;6424-6432
67. Redfield A.G., Kunz S.D. Quadrature Fourier NMR detection. Simple multiplex for dual detection and discussion. J. Magn. Reson. 19:1975;250-254
68. Sadek M., Brownlee R.T.C., Scrofani S.D.B., Wedd A.G. TOCSY assignment of broad resonances in paramagnetic proteins. J. Magn. Reson. 101:1993;309-314
69. Séry A., Housset D., Serre L., Bonicel J., Hatchikian C., Frey M., Roth M. Crystal structure of the ferredoxin I from Desulfovibrio africanus at 2.3 Å resolution. Biochemistry. 33:1994;15408-15417
70. States D.C., Haberkorn R.A., Ruben D.J. A 2-dimensional nuclear Overhauser experiment with pure absorption phase in 4 quadrants. J. Magn. Reson. 48:1982;286-292
71. 4] ferredoxin. Eur. J. Biochem. 237:1996;726-735
72. Stout C.D. Refinement of the 7Fe ferredoxin from Azobacter vinelandii at 1.9 Å resolution. J. Mol. Biol. 205:1989;545-555
73. 1H NMR determination of secondary structure for the three-iron form of ferredoxin from hyperthermophilic archaeon Pyrococcus furiosus. Biochemistry. 33:1994;6316-6326
74. Wang P.-L., Donaire A., Zhou Z.H., Adams M.W.W., La Mar G.N. Molecular model of the solution structure for the paramagnetic four-iron ferredoxin from the hyperthermophilic archaeonThermococcus litoralis. Biochemistry. 35:1996;11319-11328
75. Wishart D.S., Sykes B.D., Richards F.M. The chemical shift index a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. Biochemistry. 31:1992;1647-1651
76. Wüthrich K. NMR of Proteins and Nucleic Acids. 1986;Wiley, New York