Novel structure and redox chemistry of the prosthetic groups of the iron-sulfur flavoprotein sulfide dehydrogenase from Pyrococcus furiosus; evidencefor a [2Fe-2S] cluster with Asp(Cys)(3) ligands

The consecutive structural genes for the iron-sulfur flavoenzyme sulfide de hydrogenase, sudB and sudA, have been identified in the genome of Pyrococcu s furiosus. The translated sequences encode a heterodimeric protein with an alpha-subunit, SudA, of 52598 Da and a beta-subunit, SudB, of 30686 Da. Th e alpha-subunit carries a FAD, a putative nucleotide binding site for NADPH , and a [2Fe-2S](2+,+) prosthetic group. The latter exhibit EPR g-values, 2 .035, 1.908, 1.786, and reduction potential, E-m,E-8 = +80 mV, reminiscent of Rieske-type clusters; however, comparative sequence analysis indicates t hat this cluster is coordinated by a novel motif of one Asp and three Cys l igands. The motif is not only found in the genome of hyperthermophilic arch aea and hyperthermophilic bacteria, but also in that of mesophilic Treponem a pallidum. The beta-subunit of sulfide dehydrogenase contains another FAD, another putative binding site for NADPH, a [3Fe-4S](+,0) cluster, and a [4 Fe-4S](2+,+) cluster. The 3Fe cluster has an unusually high reduction poten tial, E-m,E-8=+230 mV. The reduced 4Fe cluster exhibits a complex EPR signa l, presumably resulting from magnetic interaction of its S=1/2 spin with th e S=2 spin of the reduced 3Fe cluster. The 4Fe cluster can be reduced with deazaflavin/EDTA/light but not with sodium dithionite; however, it is readi ly reduced with NADPH. SudA is highly homologous to KOD1-GO-GAT (or KOD1-Gl tA), a single-gene encoded protein in Pyrococcus kodakaraensis, which has b een putatively identified as hyperthermophilic glutamate synthase. However, P. furiosus sulfide dehydrogenase does not have glutamate synthase activit y. SudB is highly homologous to HydG, the gamma-subunit of P. furiosus NiFe hydrogenase. The latter enzyme also has sulfide dehydrogenase activity. Th e P. furiosus genome contains a second set of consecutive genes, sudY and s udX, with very high homology to the sudB and sudA genes, and possibly encod ing a sulfide dehydrogenase isoenzyme. Each subunit of sulfide dehydrogenas e is a primary structural paradigm for a different class of iron-sulfur fla voproteins.