The Rubredoxin from <i>Clostridium pasteurianum</i>: Mutation of the Iron Cysteinyl Ligands to Serine. Crystal and Molecular Structures of Oxidized and Dithionite-Treated Forms of the Cys42Ser Mutant

Abstract

Isolation is reported of the four mutant proteins of the electron-transfer protein rubredoxin from Clostridium pasteurianum in which each of the four cysteine ligands is changed in turn to serine. They fall into two pairs whose properties depend on whether an interior (C6, C39) or a surface (C9, C42) cysteine ligand is substituted. A crystal structure of the oxidized C42S protein (1.65 Å; R, 18.5%) confirms the presence of an FeIII(Sγ-Cys)3(Oγ-Ser) center (Fe−O, 1.82(8) Å). Significant structural change is restricted to the region around the mutation. EXAFS experiments confirm FeIIIS3O (O = Oγ-Ser or OHx) centers in each oxidized protein at pH 8. The reduction potentials of the FeIII/II couple are decreased by about 100 and 200 mV, respectively, in the interior and surface ligand mutants. The potentials are pH-dependent with respective pKared values of about 9 and 7. EXAFS data indicate an increase of 0.2−0.3 Å in the FeII−O distances in passing through these characteristic pKared values. 1H NMR experiments on CdII forms reveal the presence of CdII(S-Cys)3{O(H)-Ser} centers in the surface ligand mutants C9S and C42S by the detection of 113Cd−O−CHβ2 coupling and S−OHγ resonances. The assumption of the presence of FeII(S-Cys)3(O-Ser) centers in each mutant protein at pH values above the characteristic pKared allows a simple interpretation of the electrochemical behavior. Protonation of the Fe−Oγ-Ser link upon reduction is proposed, followed by hydrolysis at lower pH values: FeIII−Oγ-Ser + H+ + e- → FeII−Oγ(H)-Ser; FeII−Oγ(H)-Ser + H2O → FeII−OH2 + HOγ-Ser. The differences in reduction potentials, their pH dependence, and the onset of irreversible electrochemistry can be attributed to differences in the Fe−O bonds of the interior and surface ligands. These differences appear to result from variation in the conformational flexibility of the protein chelate loops which carry the ligands. An attempt to generate crystals of the reduced FeII-C42S protein by treatment of FeIII-C42S crystals with dithionite at pH 4 led to loss of iron. A crystal structure (1.6 Å; R, 16.8%) reveals that cysteine residues 6 and 9 have trapped the oxidation product SO2, a result confirmed by reactions in solution: Cys-SH + SO2 → Cys-SII−SIVO2- + H+.