MCD and 1H-NMR spectroscopic studies of Desulfovibrio africanus ferredoxin I: revised amino-acid sequence and identification of secondary structure

Determination of the structure of oxidised Desulfovibrio africanus ferredoxin I by 1H NMR spectroscopy and comparison of its solution structure with its crystal structure

The solution structure of the 64 amino acid Fe4S4 ferredoxin I from Desulfovibrio africanus has been determined using two-dimensional 1H NMR spectroscopy. Sequence-specific assignments were obtained for 59 amino acid residues and the structure determined with the program DIANA on the basis of 549 nuclear Overhauser enhancement (NOE) upper distance limits, and four dihedral angle and 52 distance constraints for the Fe4S4 cluster. The NMR structure was refined using the simulated annealing and energy minimisation protocols of the program X-PLOR to yield a final family of 19 structures selected on the basis of good covalent geometry and minimal restraint violations. The r.m.s.d. values to the average structure for this family are 0.49(+/-0.07) A and 0.94(+/-0.09) A for the backbone and heavy-atoms of residues 3 to 62, respectively. The NMR structure has been compared to the previously reported X-ray structures for the two molecules within the asymmetric unit of the crystal, which have a network of seven hydrogen bonds between them. This intermolecular interface, involving residues 38, 40 to 43 and 46, has the same conformation in the solution structures showing that the crystal packing does not perturb the structure. There are three regions in which the NMR and X-ray structures differ: around the cluster, a turn involving residues 8 to 10, and a loop involving residues 29 to 32. In the family of solution structures the backbone of the loop region incorporating residues 29 to 32 is well-defined whilst in both of the X-ray molecules it is ill-defined. The small differences between the X-ray and NMR structures for the cluster environment and the turn between residues 8 to 10 probably reflects a lack of NMR constraints. The observation of relatively rapid amide NH hydrogen exchange of NH groups close to the cluster, together with rapid flipping for Phe25, which is also close to the cluster, indicates that the cluster environment is more dynamic than the corresponding regions of related Fe/S proteins.

[3Fe-4S] <--> [4Fe-4S] cluster interconversion in Desulfovibrio africanus ferredoxin III: properties of an Asp14 --> Cys mutant

The 8Fe ferredoxin III from Desulfovibrio africanus is a monomeric protein which contains two [4Fe-4S]2+/1+ clusters, one of which is labile and can readily and reversibly lose one Fe under oxidative conditions to yield a [3Fe-4S]1+/0 cluster. This 4Fe cluster has an S = 3/2 ground sping state insteaed of S = 1/2 in the reduced +1 state [George, Armstrong, Hatchikian and Thomson (1989) Biochem. J. 264, 275-284]. The co-ordination to this cluster is unusual in that an aspartate (Asp14, D14, is found where a cysteine residue normally occurs. Using a mutant protein obtained from the overexpression in Escherichia coli of a synthetic gene in which Asp14, the putative ligand to the removable Fe, has been changed to Cys, we have studied the cluster interconversion properties of the labile cluster. Analysis by EPR and magnetic-circular-dichroism spectroscopies showed that the Asp14 --> Cys (D14C) mutant contains two [4Fe-4S]2+/1+ clusters, both with S = 1/2 in the reduced state. Also, unlike in native 8Fe D. africanus ferredoxin III, the 4Fe <--> 3Fe cluster interconversion reaction was found to be sluggish and did not go to completion. It is inferred that the reversibility of the reaction in the native protein is due to the presence of the aspartate residue at position 14 and that this residue might protect the [3Fe-4S] cluster from further degradation.

An NMR-derived model for the solution structure of oxidized Thermotoga maritima 1[Fe4-S4] ferredoxin

The solution structure of the 60-residue 1[Fe4-S4] ferredoxin from the hyperthermophilic bacterium Thermotoga maritima was determined based on 683 distance and 35 dihedral angle restraints that were obtained from NMR data. In addition, data known from crystallographic studies of ferredoxins was used for modeling of the iron-sulfur cluster and its environment. The protein shows a globular fold very similar to the fold of the related 1[Fe4-S4] ferredoxins from Desulfovibrio gigas and Desulfovibrio africanus, and elements of regular secondary structure similar to those in other ferredoxins were found in the T. maritima protein. In particular, the T. maritima protein displayed a beta-sheet structure made up of strands located at the very NH(2) and COOH termini of the protein, and an internal alpha-helix. The internal beta-sheet observed in the D. gigas and D. africanus ferredoxins could not be confirmed in T. maritima ferredoxin and is thus suggested to be only weakly present or even absent in this protein. This result suggests that thermostability in ferredoxins is not necessarily correlated with the content of stable elements of regular secondary structure.

Expression in Escherichia coli and characterization of a reconstituted recombinant 7Fe ferredoxin from Desulfovibrio africanus

Desulfovibrio africanus ferredoxin III is a monomeric protein (molecular mass of 6585 Da) that contains one [3Fe-4S]1+/0 and one [4Fe-4S]2+/1+ cluster when isolated aerobically. The amino acid sequence consists of 61 amino acids, including seven cysteine residues that are all involved in co-ordination to the clusters. In order to isolate larger quantities of D. africanus ferredoxin III, we have overexpressed it in Escherichia coli by constructing a synthetic gene based on the amino acid sequence of the native protein. The recombinant ferredoxin was expressed in E. coli as an apoprotein. We have reconstituted the holoprotein by incubating the apoprotein with excess iron and sulphide in the presence of a reducing agent. The reconstituted recombinant ferredoxin appeared to have a lower stability than that of wild-type D. africanus ferredoxin III. We have shown by low-temperature magnetic circular dichroism and EPR spectroscopy that the recombinant ferredoxin contains a [3Fe-4S]1+/0 and a [4Fe-4S]2+/1+ cluster similar to those found in native D. africanus ferredoxin III. These results indicate that the two clusters have been correctly inserted into the recombinant ferredoxin.

Identification of the iron-sulfur clusters in a ferredoxin from the archaeon Sulfolobus acidocaldarius. Evidence for a reduced [3Fe-4S] cluster with pH-dependent electronic properties

A ferredoxin isolated from the archaeon Sulfolobus acidocaldarius strain DSM 639 has been shown to contain one [3Fe-4S]1 + 10 cluster with a reduction potential of -275 mV and one [4Fe-4S]2+/1+ cluster with a reduction potential of -529 mV at pH 6.4, in the temperature range 0-50 degrees C. The monomer molecular mass was confirmed to be 10907.5 +/- 1.0 Da by electrospray mass spectrometry, as calculated from the published amino acid sequence [Minami, Y. Wakabayashi. S., Wada, K., Matsubara, H., Kerscher, L. & Oesterhelt, D. (1985) J. Biochem. (Tokyo) 97, 745-751], while the holoprotein molecular mass was found to be 11,550 +/- 1.0 Da. The reduced [3Fe-4S]0 cluster was also shown by direct electrochemistry and magnetic circular dichroic spectroscopy to undergo a one-proton uptake reaction as first observed for Azotobacter chroococcum ferredoxin I [George, S. J., Richards, A. J. M., Thomson, A. J. & Yates, M. G. (1984) Biochem. J. 224, 247-251]. The pKa of the protonation step has been determined by a novel thin film electrochemical method to be 5.8. This is significantly different from the pKa of 7.7 determined for A. vinelandii ferredoxin I [Shen, B., Martin, L. L., Butt, J. N., Armstrong, F. A., Stout, C. D., Jensen, J. M., Stephens, P. J., LaMar, G. N., Gorst, C. M. & Burgess, B. K. (1993) J. Biol. Chem. 268, 25928-25939] and indicates that the polypeptide chain around the [3Fe-4S] cluster controls this reaction. Although this appears to be only the second reported case of protonation at or near the reduced [3Fe-4S]0 cluster, its observation in S. acidocaldarius ferredoxin raises the question of the generality of this chemistry for 3Fe clusters. The similarity of the pKa to the estimated intracellular pH of S. acidocaldarius strongly suggests a physiological role for this process.

Determination of the [Fe4S4]Cys4 cluster geometry of Desulfovibrio africanus ferredoxin I by 1H NMR spectroscopy

1D and 2D 1H NMR studies of the Fe4S4 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 beta CH 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 beta CH resonances with a Karplus-type equation relating the shifts to iron-sulfur-beta carbon-beta proton dihedral angles, taken together with the relative relaxation rates of the two beta CH2 resonances, estimated from their linewidths, then allowed the iron-sulfur-beta-carbon-alpha-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 ferredoxins even though there are differences in their 1H NMR spectra. The sequence-specific and stereospecific assignments have been extended by analogy to the related Fe4S4-containing D. gigas ferredoxin I, and the stereospecific assignments to the Fe4S4-containing Thermococcus litoralis ferredoxin.