High-resolution crystal structures of two polymorphs of cytochrome c' from the purple phototrophic bacterium Rhodobacter capsulatus

Journal of Molecular Biology

Volumn 259, Issue 3, 1996, Pages 467-479

  Tahirov, Tahir H ^a,c   Misaki, Shintaro ^a   Meyer, Terry E ^b   Cusanovich, Michael A ^b   Higuchi, Yoshiki ^a,d   Yasuoka, Noritake ^a  

^a UNIVERSITY OF HYOGO   (Japan)

^b University of Arizona   (United States)

^c INSTITUTE OF PHYSICS   (Azerbaijan)

^d KYOTO UNIVERSITY   (Japan)

Author keywords

Cytochrome c'; Electron transfer protein; Protein structure; Rhodobacter capsulatus; X ray crystallography

Indexed keywords

CYTOCHROME C; PROTEIN SUBUNIT;

AMINO ACID SEQUENCE; ARTICLE; CRYSTAL STRUCTURE; ELECTRON TRANSPORT; NONHUMAN; PHOTOTROPHIC BACTERIUM; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE; RHODOBACTER CAPSULATUS; X RAY CRYSTALLOGRAPHY;

ACHROMOBACTER; ACHROMOBACTER DENITRIFICANS; ALCALIGENES; ALLOCHROMATIUM VINOSUM; BACTERIA (MICROORGANISMS); CHROMATIUM; PHAEOSPIRILLUM MOLISCHIANUM; PHOTOBACTERIA; RHODOBACTER CAPSULATUS; RHODOPSEUDOMONAS; RHODOSPIRILLUM RUBRUM;

EID: 0029940242     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0333     Document Type: Article

References (37)

1. Abola, F. C., Bernstein, F. C., Bryant, S. H., Koetzle, T. F. & Weng, J. (1987). Crystallographic Databases - Information Content, Software Systems, Scientific Applications, pp. 107-132, Data Commission of the International Union of Crystallography, Bonn, Cambridge and Chester.
2. Ambler, R. P., Bartsch, R. G., Daniel, M., Kamen, M. D., McLellan, L., Meyer, T. E. & Van Beeumen, J. (1981). Amino acid sequences of bacterial cytochromes c' and c-556. Proc. Natl Acad. Sci. USA, 78, 6854-6857.
3. Baker, E., Anderson, B. F., Dobbs, A. J. & Dodson, E. J. (1995). Use of iron anomalous scattering with multiple models and data sets to identify and refine a weak molecular replacement solution: structure analysis of cytochrome c' from two bacterial species. Acta Crystallog. sect. D, 51, 282-289.
4. Bartsch, R. G. (1978). Cytochromes. In The Photosynthetic Bacteria (Clayton R. K. & Sistrom, W. R., eds), pp. 249-280, Plenum, New York.
5. Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Jr, Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). The protein data bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
6. Brunger, A. T. (1990a). Extension of molecular replacement: a new search strategy based on Patterson correlation refinement. Acta Crystallog. sect. A, 46, 46-57.
7. Brunger, A. T. (1990b). XPLOR Manual Version 2.1, Yale University New Haven.
8. Caffrey M., Simorre, J.-P, Brutscher, B., Cusanovich, M. & Marion, D. (1995). NMR assignment of Rhodobacter capsulatus ferricytochrome c', a 28 kDa paramagnetic heme protein. Biochemistry, 34, 5904-5912.
9. Cusanovich, M. A. (1971). Molecular weights of some cytochromes c'. Biochim. Biophys. Acta, 236, 238-241.
10. Cusanovich, M. A., Meyer, T. E. & Tollin, G. (1987). c-Type cytochromes: oxidation-reduction properties. Advan. Bioinorg. Chem. 7, 37-91.
11. Doyle, M. L., Weber, P. C. & Gill, S. J. (1985). Carbon monoxide binding to Rhodospirillum molischianum ferrocytochrome c'. Biochemistry, 24, 1987-1991.
12. Doyle, M. L., Gill, S. J. & Cusanovich, M. A. (1986). Ligand controlled dissociation of Chromatium vinosum cytochrome c'. Biochemistry, 25, 2509-2516.
13. Engh, R. A. & Huber, R. (1991). Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallog. sect. A, 47, 392-400.
14. Finzel, B. C., Weber, P. C., Hardman, K. D. & Salemme, F. R. (1985). Structure of ferricytochrome c' from Rhodospirillum molischianum at 1.67 Å resolution. J. Mol. Biol. 186, 627-643.
15. Higuchi, Y., Okama, Y., Kanda, T., Misaki, S., Yasuoka, N., Meyer, T. E. & Cusanovich, M. A. (1996). Crystallization and preliminary X-ray study of a new crystal form of cytochrome c' from Rhodobacter capsulatus. Acta Crystallog. sect. D, 52, 199-200.
16. Hodel, A., Kim, S. H. & Brunger, A. T. (1992). Model bias in macromolecular crystal structures. Acta Crystallog. sect. A, 48, 851-858.
17. Jancarik, J. & Kim, S.-H. (1991). Sparse matrix sampling: a screening method for crystallization of proteins. J. Appl Crystallog. 24, 409-411.
18. Kassner, R. J. (1991). Ligand binding properties of cytochromes c'. Biochim. Biophys. Acta, 1058, 8-12.
19. Lakowski, 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. Crystallog. 26, 283-291.
20. La Mar, G. N., Jackson, J. T., Dugad, L. B., Cusanovich, M. A. & Bartsch, R. G. (1990). Proton NMR study of the comparative electron/magnetic properties and dynamics of the acid - alkaline transition in a series of ferricytochromes c'. J. Biol. Chem. 265, 16173-16180.
21. Maltempo, M. M. (1974). Magnetic state of an unusual bacterial heme protein. J. Chem. Phys. 61, 2540-2547.
22. Matthews, B. W. (1968). Solvent content of protein crystals. J. Mol. Biol. 33, 491-497.
23. McPherson, A. (1982). Preparation and Analysis of Protein Crystals. pp. 94-97, John Wiley & Sons, New York.
24. Meyer, T. E. & Kamen, M. D. (1982). New perspectives on c-type cytochromes. Advan. Protein Chem. 35, 105-212.
25. Monkara, F., Bingham, S. J., Kadir, F. H. A., McEwan, A. G., Thomson, A. J., Thurgood, A. G. P. & Moore, G. R. (1992). Spectroscopic studies of Rhodobacter capsulatus cytochrome c' in the isolated state and in intact cells. Biochim. Biophys. Acta, 1100, 184-188.
26. Patel, M. J., Kassner, R. J., Meyer, T. E. & Cusanovich, M. (1989). Steric and hydrophobic effects in alkyl isocyanide binding to Rhodospirillum molischianum cytochrome c'. Biochemistry, 28, 2140-2144.
27. Otwinowski, Z. (1986). DENZO. An Oscillation Data Processing Program for Macromolecular Crystallography. Yale University Connecticut.
28. Ren, Z., Meyer, T. & McRee, D. E. (1993). Atomic structure of cytochrome c' with an unusual ligand-controlled dimer dissociation at 1.8 Å resolution. J. Mol. Biol. 234, 433-445.
29. Rubinov, S. C. & Kassner, R. J. (1984). Cytochromes c' in their reaction with ethyl isocyanide. Biochemistry, 23, 2590-2595.
30. Sakabe, N. (1991). X-ray diffraction data collection system for modern protein crystallography with a Weissenberg camera and an imaging plate using synchrotron radiation. Nucl. Instrum. Methods Phys. Res. Ser. A, 303, 448-463.
31. Scheidt, R. W. & Reed, C. A. (1981). Spin-state/stereochemical relationships in iron porphyrins: implications for the heme proteins. Chem. Rev. 81, 543-555.
32. Scheidt, R. W., Haller, K. J., Fons, M., Mashiko, T. & Reed, C. A. (1981). A (carbonmonoxy)heme complex with a weak proximal bond. Molecular stereochemistry of carbonyl(deuteroporphinato) (tetrahydrofuran)-iron(II). Biochemistry, 20, 3653-3657.
33. Valentine, J. S., Sheridan, R. P., Allen, L. G. & Kahn, P. C. (1979). Coupling between oxidation state and hydrogen bond conformation in heme proteins. Proc. Natl Acad. Sci. USA, 76, 1009-1013.
34. Weber, P. & Salemme, F. R. (1977). Preliminary crystallographic data for cytochromes c' of Rhodopseudomonas capsulata and Rhodospirillum molischianum. J. Mol. Biol. 117, 815-820.
35. Weber, P. C., Bartsch, R. G., Cusanovich, M. A., Hamlin, R. C., Howard, A., Jordan, S. R., Kamen, M. D., Meyer, T. E., Weatherford, D. W., Xuong, N. H. & Salemme, F. R. (1980). Structure of cytochrome c': a dimeric, high-spin haem protein. Nature, 286, 302-304.
36. Weber, P. C., Howard, A., Xuong, N. H. & Salemme, F. R. (1981). Crystallographic structure of Rhodospirillum molischianum ferricytochrome c' at 2.5 Å resolution. J. Mol. Biol. 153, 399-424.
37. Yasui, M., Harada, S., Kai, Y., Kasai, N., Kusunoki, M. & Matsuura, Y. (1992). Three-dimensional structure of ferricytochrome c' from Rhodospirillum rubrum at 2.8 Å resolution. J. Biochem. 111, 317-324.