A proton-NMR investigation of the fully reduced cytochrome c7 from Desulfuromonas acetoxidans. Comparison between the reduced and the oxidized forms

European Journal of Biochemistry

Volumn 266, Issue 2, 1999, Pages 634-643

  Assfalg, Michael ^c   Banci, Lucia ^c   Bertini, Ivano ^b   Bruschi, Mireille ^a   Giudici Orticoni, Marie T ^a   Turano, Paola ^c  

^a CNRS   (France)

^b UNIVERSITY OF FLORENCE   (Italy)

^c NONE

Author keywords

Multiheme cytochrome; NMR; Reduction potentials; Solution structure

Indexed keywords

CYTOCHROME C; CYTOCHROME C3; HEME; CYTOCHROME C(3); CYTOCHROME C7; LIGAND; OXYGEN; PROTON;

ANALYTIC METHOD; ARTICLE; OXIDATION; PRIORITY JOURNAL; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; REDUCTION; STRUCTURE ANALYSIS; AMINO ACID SEQUENCE; CHEMICAL STRUCTURE; CHEMISTRY; CRYSTALLOGRAPHY; DELTAPROTEOBACTERIA; METABOLISM; MOLECULAR GENETICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; OXIDATION REDUCTION REACTION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; CRYSTALLOGRAPHY; CRYSTALLOGRAPHY, X-RAY; CYTOCHROME C GROUP; DELTAPROTEOBACTERIA; HEME; LIGANDS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; OXIDATION-REDUCTION; OXYGEN; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTONS; THERMODYNAMICS;

EID: 0000988375     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1432-1327.1999.00904.x     Document Type: Article

References (54)

1. 7) from the green photosynthetic bacterium Chloropseudomonas ethylica. FEBS Lett. 18, 351-353.
2. 3 (Mr 26,000) isolated from sulfate-reducing bacteria and its relationship to other cytochromes from Desulfovibrio. Methods Enzymol. 243, 140-155.
3. 7) from Desulfuromonas acetoxidans. Biochim. Biophys. Acta 460, 58-64.
4. 4. Pereira, I.A.C., Pacheco, I., Liu, M.-Y., LeGall, J., Xavier, A.V. & Tereira, M. (1997) Multiheme cytochromes from the sulfur-reducing bacterium Desulfuromonas acetoxidans. Eur. J. Biochem. 248, 323-328.
5. 5. Brugna, M., Nitschke, W., Tui, H., Bruschi, M. & Giudici-Orticoni, M.T. (1999) First evidence for the presence of a hydrogenase in sulphur-reducing bacterium Desulfuromonas acetoxidans. J. Bacteriol. 181, 5505-5508.
6. 7 from Desulfuromonas acetoxidans. Proc. Natl Acad. Sci. USA 93, 14396-14400.
7. 7 from Desulfuromonas acetoxidans. Eur. J. Biochem. 256, 261 -270.
8. 3. Structural hypothesis of an intramolecular electron transfer pathway within a tetra-heme cytochrome. J. Mol. Recogn. 4, 27-33.
9. 7 produced in Desulfovibrio desulfuricans retains its metal reductase activity. Appl. Environ. Microbiol. 64, 1308-1312.
10. 551.5 from Desulfuromonas acetoxidans. Biochim. Biophys. Acta 579, 269-278.
11. 3. Biochem. Biophys. Res. Commun. 120, 384-389.
12. 12. Piotto, M., Saudek, V. & Sklenar, V. (1992) Gradient-tailored excitation for single quantum NMR spectroscopy of aqueous solutions. J. Biomol. NMR 2, 661-666.
13. 13. Macura, S., Wüthrich, K. & Ernst, R.R. (1982) The relevance of J cross-peaks in two-dimensional NOE experiments of macromolecules. J. Magn. Reson. 47, 351-357.
14. 14. Marion, D. & Wüthrich, K. (1983) Application of phase sensitive correlated spectroscopy (COSY) for measurements of proton-proton spin-spin coupling constants in proteins. Biochem. Biophys. Res. Commun. 113, 967-974.
15. 15. Eccles, C., Güntert, P., Billeter, M. & Wüthrich, K. (1991) Efficient analysis of protein 2D NMR spectra using the software package EASY. J. Biomol. NMR 1, 111-130.
16. 16. Güntert, P., Braun, W. & Wüthrich, K. (1991) 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, 517-530.
17. 17. Güntert, P., Mumenthaler, C. & Wüthrich, K. (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol. 273, 283-298.
18. 3 from Desulfovibrio vulgaris Hildenborough at 1.9 Angstrom resolution. J. Mol. Biol. 234, 680-699.
19. 19. Morais, J., Palma, P.N., Frazao, C., Caldeira, J., LeGall, J., Moura, I., Moura, J.J.G. & Carrondo, M.A. (1995) Structure of the tetraheme cytochrome from Desulfovibrio desulfuricans ATCC 27774: X-ray diffraction and electron paramagnetic resonance studies. Biochemistry 34, 12830-12841.
20. 3 at 1.8 Angstroms resolution. J. Mol. Biol. 172, 109-139.
21. 3 from Desulfovibrio vulgaris Hildenborough at 2 Angstroms resolution. J. Bioehem. (Tokyo) 110, 532.
22. 3 (M(r) 26,000) from Desulfovibrio desulfuricans Norway. Structure 4, 395-404.
23. 3 from Desulfovibrio gigas: crystal structure at 1.8 Å resolution and evidence for a specific calcium binding site. Protein Sci. 5, 1342-1354.
24. 3 from Desulfovibrio desulfuricans Norway at 1.7 Å resolution. J. Mol. Biol. 243, 653-667.
25. 25. Pearlman, D.A., Case, D.A., Caldwell, G.C., Siebel, G.L., Singh, U.C., Weiner, P. & Kollman, P.A. (1991) AMBER 4.0, University of California, San Francisco.
26. 26. Pearlman, D.A., Case, D.A., Caldwell, J.W., Ross, W.S., Cheatham, T.E., Ferguson, D.M., Seibel, G.L., Singh, U.C., Weiner, P.K. & Kollman, P.A. (1995) AMBER 4.1, University of California, San Francisco.
27. 27. Laskowski, R.A., Rullmann, J.A.C., MacArthur, M.W., Kaptein, R. & Thornton, J.M. (1996) AQUA and PROCHECKNMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 8, 477-486.
28. 28. Klapper, T., Hagstrom, R., Fine, R., Sharp, K. & Honig, B. (1986) Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification. Proteins Struct. Funct. Genet. 1, 47-59.
29. 29. Gilson, M.K., Rashin, A., Fine, R. & Honig, B. (1985) On the calculation of electrostatic interactions in proteins. J. Mol. Biol. 183, 503-516.
30. 30. Nicholls, A. & Honig, B. (1991) A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. J. Comp. Chem. 12, 435-445.
31. 31. Banci, L., Bertini, I., Huber, J.G., Spyroulias, G.A. & Turano, P. (1999) Solution structure of reduced horse heart cytochrome c. J. Biol. Inorg. Chem. 4, 21-31.
32. 5. Eur. J. Biochem. 249, 270-279.
33. 33. Warwicker, J. & Watson, H.C. (1982) Calculation of the electric potential in the active site cleft due to alpha helix dipoles. J. Mol. Biol. 157, 671-682.
34. 34. Gilson, M.K., Sharp. K.A. & Honig, B. (1987) Calculating the electrostatic potential of molecules in solution: method and error assessment. J. Comp. Chem. 9, 327-335.
35. 35. Gilson, M.K. & Honig, B. (1988) Energetics of charge-charge interactions in proteins. Proteins 3, 32-52.
36. 36. Gilson, M.K. & Honig, B. (1988) Total electrostatic energy of a protein. Proteins 4, 7-18.
37. 37. Coutinho, I. & Xavier, A.V. (1994) Tetraheme cytochromes. Methods Enzymol. 243, 119-140.
38. 1H NMR. J. Biol. Inorg. Chem. 1, 305-311.
39. 3: structural basis for functional cooperatively. J. Mol. Biol. 281, 719-739.
40. 40. Lin, L.-Y., Park, H.I. & Ming, L.-J. (1997) Metal-binding and active-site structure of di-zinc Streptamices griseus aminopeptidase. J. Biol. Inorg. Chem. 2, 744-749.
41. 3. Nature (London) 282, 806-810.
42. 42. Rodgers, K.R., Arafa, I.M. & Goff, H.M. (1990) Iron porphyrin catalyzed oxidation of propanal and cyclohexene by molecular oxygen. J. Chem. Soc. Chem. Commun. 1323-1324.
43. 43. Borgias, B., Thomas, P.D. & James, T.L. (1989) Complete Relaxation Matrix Analvsis (CORMA). University of California, San Francisco.
44. 1H chemical shifts as structural parameters in some low spin ferriheme proteins. J. Biol. Inorg. Chem. 4, 515-519.
45. 7). Eur. J. Biochem. 144, 433-440.
46. 46. Antosiewicz, J., McCammon, J.A. & Gilson, M.K. (1994) Prediction of pH-dependent properties of proteins. J. Mol. Biol. 238, 415-436.
47. 47. Heering, H.A., Bulsink, Y.B.M., Hagen, W.R. & Meyer, T.E. (1995) Influence of charge and polarity on the redox potentials of high-potential iron-sulfur proteins: evidence for the existence of two groups. Biochemistry 34, 14675-14686.
48. 48. Gunner, M.R. & Honig, B. (1991) Electrostatic control of midpoint potentials in the cytochrome subunit of the Rhodopseudomonas viridis reaction center. Proc. Natl Acad. Sci. USA 88, 9151-9155.
49. 4 ferredoxins. Inorg. Chem. 35, 4248-4253.
50. 3 from Desulfovibrio vulgaris Hildenborough. J. Biol. Inorg. Chem. 2, 714-727.
51. 3 and Fe-only hydrogenase from Desulfovibrio vulgaris Hildenborough. Proteins 33, 590-600.
52. 52. Guerlesquin, F., Dolla, A. & Bruschi, M. (1994) Involvement of electrostatic interactions in cytochrome c complex formations. Biochimie 76, 515-523.
53. 53. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291.
54. 54. Koradi, R., Billeter, M. & Wüthrich, K. (1996) MOLMOL: a program for display and analysis of macromolecular structure. J. Mol. Graphics 14, 51-55.