CRYSTAL-STRUCTURE OF THE FERREDOXIN-I FROM DESULFOVIBRIO-AFRICANUS AT2.3 ANGSTROM RESOLUTION

The crystal structure of the ferredoxin I from the sulfate-reducing ba cterium Desulfovibrio africanus (DaFdI) has been solved and refined by X-ray diffraction. The crystals are orthorhombic with n = 96.6 Angstr om, b = 58.1 Angstrom, and c = 20.7 Angstrom, space group P2(1)2(1)2, and two ferredoxin molecules per asymmetric unit. The initial electron density map has been obtained by combining phasing by molecular repla cement methods, anomalous scattering, and noncrystallographic averagin g. The final crystallographic R factor is 0.182 with 10-2.3 Angstrom r esolution data. Ln parallel, the amino acid sequence was redetermined. This showed that DaFdI contains 64 residues (instead of 61) including one free cysteine, one histidine, and one tryptophan in the C-termina l part of the molecule. The current molecular model includes the two m olecules of the asymmetric unit, 67 water molecules, and one sulfate i on. The DaFdI overall folding very closely resembles that of ferredoxi ns of known structure. Comparisons with the single cluster ferredoxins from Desulfovibrio gigas and Bacillus thermoproteolyticus show that t he presence or the absence of a disulfide bridge does not significantl y affect the folding of the other half of the molecule, including the characteristic a-helix of the single cluster ferredoxins. Like other f erredoxins or analogs, the [4Fe-4S] iron-sulfur cluster presents, at 2 .3 Angstrom resolution, a cubane-like geometry. By contrast, its immed iate environment is different as it includes, besides the four cysteic sulfur ligands, the sulfur atom of the free cysteine. This sulfur ato m, which is buried within the protein, is in van der Waals contact wit h one labile sulfur of the cluster and one liganded cysteic sulfur. Th e association of a [4Fe-4S] cluster with one free cysteic sulfur is si milar to that previously found in both X-ray structures of Azotobacter vinelandii and Peptococcus aerogenes [Stout, C. D. (1989) J. Mol. Bio l. 205, 545-555; Backes, G., et al. (1991) J. Am. Chern. Sec. 113, 205 5-2064]. Chemical sequence analysis suggests that this characteristic [4Fe-4S] cluster sulfur environment is widely distributed among ferred oxins.