Structure of dimeric cytochrome c₃ from Desulfovibrio gigas at 1.2 Å resolution

The structure of dimeric cytochrome c₃ from the sulfate-reducing bacterium Desulfovibrio gigas, diDg, obtained by ab initio methods was further refined to 1.2 Å resolution, giving final reliability factors of R_free = 14.8% and R = 12.4%. This cytochrome is a dimer of tetraheme cytochrome c₃ molecules covalently linked by two solvent-accessible disulfide bridges, a characteristic unique to members of the cytochrome c₃ superfamily. Anisotropic analysis using the semi-rigid TLS method shows different behaviour for analogous loops in each monomer arising from their different packing environments. A detailed sequence and structural comparison with all other known cytochrome c₃ domains in single- and multi-domain cytochromes c₃ shows the presence of structurally conserved regions in this family, despite the high variability of the amino-acid sequence. An internal water molecule is conserved in a common structural arrangement in all c₃ tetraheme domains, indicating a probable electron-transfer pathway between hemes I and II. Unique features of diDg are an internal methionine residue close to heme I and to one of the axial ligands of heme III, where all other structures of the cytochrome c₃ superfamily have a phenylalanine, and a rather unusual CXXXCH heme-binding motif only found so far in this cytochrome.