Solution structure of an artificial Fe₈S₈ ferredoxin : the D13C variant of Bacillus schlegelii Fe₇S₈ ferredoxin

Abstract

The solution structure of the D13C variant of the thermostable Fe 7 S 8 ferredoxin from Bacillus schlegelii has been determined by 1 H-NMR spectroscopy in its oxidized form. In a variable-temperature NMR study the D13C variant was as thermostable (up to 90°C) as the wild-type protein (WT). Seventy-five out of 77 amino acid residues and 81% of all theoretically expected proton resonances in the D13C Fe 8 S 8 protein have been assigned. Its structure was determined through torsion angle dynamics calculations with the program DYANA, using 935 meaningful NOEs (from a total of 1251), hydrogen bond constraints, and NMR-derived dihedral angle constraints for the cluster-ligating cysteines. Afterwards, restrained energy minimization and restrained molecular dynamics were applied to each conformer of the family. The final family of 20 structures has RMSD values from the mean structure of 0.055 nm for the backbone atoms and of 0.099 nm for all heavy atoms. The overall folding of the WT is maintained in the mutant, except for the immediate vicinity of the new cysteine, which becomes much more similar to native Fe 8 S 8 proteins. The two residues at positions 11 and 12, which constitute an insertion with respect to all known Fe 8 S 8 proteins, assume a conformation that does not prevent the preceding and following residues from folding like in native Fe 8 S 8 proteins. Clear evidence for the existence of two conformations involving almost half of the amino acid residues was found. The two conformations are structurally indistinguishable. Temperature-dependent NMR experiments show that one of them is thermodynamically more stable than the other.

Identification and Characterization of PshB, the Dicluster Ferredoxin that Harbors the Terminal Electron Acceptors FA and FB in Heliobacterium modesticaldum,

“…A database search shows that PshB is a member of a family of a large number of bacterial dicluster ferredoxins that are highly acidic and have nearly the same mass and number of amino acids. A number of high-resolution X-ray and NMR structures are available for several bacterial dicluster ferredoxins (pdb entries 1FDX (now replaced with 1DUR), 1CLF, 1FDN, 2FDN, 1BLU, 1FCA, 5FD1, 1BC6, 1BQX, 1RGV) (31)(32)(33)(34)(35)(36)(37)(38)(39)(40)(41), including PsaC (pdb entry 1K0T) (42). In bacterial dicluster ferredoxins as well as PsaC, both [4Fe-4S] 1+,2+ cluster binding motifs and the clusters themselves exhibit a local pseudo-C 2 -symmetry.…”

Solution structure of paramagnetic metalloproteins

“…Many Fe-S proteins have then been studied with similar procedures, including the HiPIP from C. vinosum [34,35], the Fe 8 S 8 ferredoxin from C. pasteurianum [30,36], the Fe 7 S 8 ferredoxin from B. schlegelii [25] and its arti®cial Fe 8 S 8 derivative [37], some Fe 4 S 4 [38±40] and Fe 2 S 2 [41±43] ferredoxins, the rubredoxin from C. pasteurianum [44], and some mutants of the above proteins [45,46]. Many paramagnetic cytochromes have also been studied (recently reviewed in [47]).…”