Crystal structure of the 2[4Fe-4S] ferredoxin from Chromatium vinosum: Evolutionary and mechanistic inferences for [3/4Fe-4S] ferredoxins

Protein Science

Volumn 5, Issue 9, 1996, Pages 1765-1775

  Moulis, Jean Marc ^a   Sieker, Larry C ^b   Wilson, Keith S ^c,d   Dauter, Zbigniew ^c,d  

^a CEA GRENOBLE   (France)

^b UNIVERSITY OF WASHINGTON   (United States)

^c EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^d UNIVERSITY OF YORK   (United Kingdom)

Author keywords

Chromatium vinosum; crystal structure; electron transfer; evolution; ferredoxin; hydrogen bond; iron sulfur

Indexed keywords

FERREDOXIN;

AMINO TERMINAL SEQUENCE; ANAEROBIC METABOLISM; ARTICLE; CHROMATIUM VINOSUM; CRYSTAL STRUCTURE; ELECTRON TRANSPORT; EVOLUTION; GENE CLUSTER; GENE REARRANGEMENT; HYDROGEN BOND; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; SYNCHROTRON;

EID: 0029786946     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560050902     Document Type: Article

References (39)

1. Adman ET, Sieker LC, Jensen LH. 1973. The structure of a bacterial ferredoxin. J Biol Chem 248:3987-3996.
2. Adman ET, Sieker LC, Jensen LH. 1976. Structure of Peptococcus aerogenes ferredoxin. Refinement at 2 Å resolution. J Biol Chem 251:3801-3806.
3. Bachofen R, Arnon DI 1966. Crystalline ferredoxin from the photosynthetic bacterium Chromatium. Biochim Biophys Acta 120:259-265.
4. 4 clusters in ferredoxins and high-potential iron proteins. New information from X-ray crystallography and resonance Raman spectroscopy. J Am Chem Soc 113:2055-2064.
5. Bernstein FC, Koetzle TF, Williams GJB, Meyer EF Jr, Brice MD, Rodgers JR, Kennard O, Simanouchi T, Tasumi M. 1977. The Protein Data Bank: A computer-based archival file for macromolecular structures. J Mol Biol 112:535-542.
6. Bertini I, Donaire A, Feinberg BA, Luchinat C, Piccioli M, Yuan H. 1995 Solution structure of the oxidised 2[4Fe-4S] ferredoxin from Clostridium pasteurianum. Eur J Biochem 232:192-205.
7. Cammack R. 1992 Iron clusters in enzymes. Adv Inorg Chem 38:281-322.
8. 4*clusters in high-potential iron protein and in ferredoxin. Proc Natl Acad Sci USA 69:3526-3529.
9. CCP4. 1994. Collaborative Computational Project, Number 4. The CCP4 suite. Programs for protein crystallography. Acta Crystollogr D 50:760-763.
10. Duée ED, Fanchon E, Vicat J, Sieker LC, Meyer J, Moulis JM. 1994. Refined crystal structure of the 2[4Fe-4S] ferredoxin from Clostridium acidurici at 1.84 Å resolution. J Mol Biol 243:683-695.
11. Engh RA, Huber R. 1991 Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallogr A 47:392-400.
12. Fukuyama K, Matsubara H, Tsukihara T, Katsube Y. 1989. Structure of [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus refined at 2.3 Å resolution. J Mol Biol 210:383-398.
13. Fukuyama K, Nagahara Y, Tsukihara T, Katsube Y, Hase T, Matsubara H. 1988. Tertiary structure of Bacillus thermoproteolyticus [4Fe-4S] ferredoxin. Evolutionary implications for bacterial ferredoxins. J Mol Biol 199:183-193.
14. Gaillard J, Quinkal I, Moulis JM. 1993. Effect of replacing conserved proline residues on the EPR and NMR properties of Clostridium pasteurianum 2[4Fe-4S] ferredoxin. Biochemistry 32:9881-9887.
15. Holm L, Sander C. 1993. Protein structure comparison by alignment of distance matrices. J Mol Biol 233:123-138.
16. Huber JG, Gaillard J, Moulis JM 1995 NMR of Chromatium vinosum ferredoxin: Evidence for structural inequivalence and impeded electron transfer between the two [4Fe-4S] clusters. Biochemistry 34:194-205.
17. Jones TA. 1978. A graphics model building and refinement system for macromolecules. J Appl Crystallogr 11:268-272.
18. Kissinger CR, Sieker LC, Adman ET, Jensen LH. 1991. Refined crystal structure of ferredoxin II from Desulfovibrio gigas at 1.7 Å J Mol Biol 219:693-715.
19. Konnert JH, Hendrickson WA 1980 A restrained-parameter thermal-factor refinement procedure. Acta Crystallogr A 36:344-350.
20. Kraulis PJ. 1991. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 24:946-950.
21. Lamzin VS, Wilson KS 1993. Automated refinement of protein models. Acta Crystallogr D 49:129-147.
22. Laskowski RA, MacArthur MW, Moss DS, Thornton JM. 1993. PROCHECK: A program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283-291.
23. Marcus RA, Sutin N. 1985. Electron transfers in chemistry and biology. Biochim Biophys Acta 811:265-322.
24. Matsubara H, Saeki K. 1992. Structural and functional diversity of ferredoxins and related proteins. Adv Inorg Chem 38:223-280.
25. Matthews BW. 1968. Solvent content of protein crystals. J Mol Biol 33:491-497.
26. Moulis JM. 1996 Molecular cloning and expression of the gene encoding Chromatium vinosum 2[4Fe-4S] ferredoxin. Biochim Biophys Acta. Forthcoming.
27. Moulis JM, Davasse V. 1995. Probing the role of electrostatic forces in the interaction of Clostridium pasteurianum ferredoxin with its redox partners. Biochemistry 34:16781-16788.
28. 2+/3+ high-potential iron-sulfur protein from Chromatium vinosum. Biochemistry 27:8712-8719.
29. Mavaza J. 1994. AMoRe: An automated package for molecular replacement. Acta Crystallogr A 50:157-163
30. Otaka E, Ooi T. 1987. Examination of protein sequence homologies: IV. Twenty seven bacterial ferredoxins. J Mol Evol 26:257-267
31. Otwinowski Z, Minor W. 1994. DENZO: A film processing program for macromolecular crystallography. New Haven, Connecticut: Yale University.
32. Pétillot Y, Forest E, Meyer J, Moulis JM. 1995. Observation of holoprotein molecular ions of several ferredoxins by electrospray-ionization mass spectrometry. Anal Biochem 228:56-63.
33. Read RJ. 1986. Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallogr A 42:140-149.
34. Séry A, Housset D, Serre L, Bonicel J, Hatchikian C, Frey M, Roth M. 1994. Crystal structure of the ferredoxin I from Desulfovibrio africanus at 2.3 Å resolution. Biochemistry 33:15408-15417.
35. Sheldrick GM, Schneider TR. 1996. SHELXL: High-resolution refinement. Methods Enzymol. Forthcoming.
36. Sieker LC. 1988. Interesting observations on the nature of protein crystals and their growth. J Crystal Growth 90:31-38.
37. Smith ET, Feinberg BA. 1990. Redox properties of several bacterial ferredoxins using square wave voltammetry. J Biol Chem 265:14371-14376.
38. Stout CD. 1989. Refinement of the 7 Fe ferredoxin from Azotobacter vinelandii at 1.9 Å resolution. J Mol Biol 205:545-555.
39. Wilson AJC. 1942 Determination of absolute from relative X-ray data intensities. Nature (Lond) 150:151-152