Determination of the [Fe 4S 4]Cys 4 cluster geometry of Desulfovibrio africanus ferredoxin I by 1H NMR spectroscopy

Abstract

1D and 2D 1H NMR studies of the Fe 4S 4, cluster containing ferredoxin I from Desulfovibrio africanus have been carried out with the aim of determining the geometry of the cluster linkages with the 4 Cys side chains that bind the cluster. This required the Cys βCH resonances of the oxidised protein to be sequence-specifically and stereo-specifically assigned, and this was accomplished by a combination of TOCSY and NOE measurements, allied to model building based on X-ray structures of related ferredoxins. An analysis of the estimated hyperfine shifts of the Cys βCH resonances with a Karplus-type equation relating the shifts to iron-sulfur-β carbon-/3 proton dihedral angles, taken together with the relative relaxation rates of the two βCH 2 resonances, estimated from their linewidths, then allowed the ironsulfur-/3-carbon-α-carbon dihedral angles to be determined. A novel representation of the NMR data is presented which shows that the cluster dihedral angles are uniquely determined by the NMR data. The analysis reveals that the dihedral angles for D. africanus ferredoxin I are similar to the corresponding angles of other ferrredoxins even though there are differences in their 1H NMR spectra. The sequence-specific and stereospecific assignments have been extended by analogy to the related Fe 4S 4-containing D. gigas ferredoxin I, and the stereospecific assignments to the Fe 4S 4-containing Thermococcus litoralis ferredoxin.