Cytochrome c₃ from Desulfovibrio gigas: Crystal structure at 1.8 Å resolution and evidence for a specific calcium‐binding site

Abstract

Crystals of the tetraheme cytochrome c3 from sulfate-reducing bacteria Desulfovibrio gigas (Dg) (MW 13 kDa, 11 1 residues, four heme groups) were obtained and X-ray diffraction data collected to 1.8 A resolution. The structure was solved by the method of molecular replacement and the resulting model refined to a conventional R-factor of 14.9%. The three-dimensional structure shows many similarities to other known crystal structures of tetraheme c3 cytochromes, but it also shows some remarkable differences. In particular, the location of the aromatic residues around the heme groups, which may play a fundamental role in the electron transfer processes of the molecule, are well conserved in the cases of hemes I, 111, and IV. However, heme I1 has an aromatic environment that is completely different to that found in other related cytochromes c 3 . Another unusual feature is the presence of a Ca2+ ion coordinated by oxygen atoms supplied by the protein within a loop near the N-terminus. It is speculated that this loop may be stabilized by the presence of this CaZ+ ion, may contribute to heme-redox perturbation, and might even be involved in the specificity of recognition with its redox partner.

800 MHz 1H NMR solution structure refinement of oxidized cytochrome c7 from Desulfuromonas acetoxidans

“…A comparison with those of 4-heme and 8-heme cytochromes c 3 from Desulfovibrio, as they result from the analysis of the crystal structures, is also reported. High-resolution (1.7Ϫ2.2 Å ) X-ray structures are available for the tetraheme cytochromes from D. desulfuricans (ATCC 27774 [16] and Norway strain [21]), Desulfovibrio gigas [20], Desulfovibrio vulgaris (Hildenborough [15] and Miyazaki [17]), and for an octaheme cytochrome from D. desulfuricans [19]. The latter protein is a dimeric protein, each subunit containing four hemes.…”

Solution structure of Desulfovibrio vulgaris (Hildenborough) ferrocytochrome c 3 : structural basis for functional cooperativity 1 1Edited by P. E. Wright

“…This is still the case for the tetrahaem cytochromes c 3 from Desulfovibrio spp., even though considerable progress has been made in rationalising their thermodynamic properties (Santos et al, 1984;Coletta et al, 1991;Turner et al, 1994Turner et al, , 1996Park et al, 1996;Louro et al, 1996;Salgueiro et al, 1997) and high-resolution X-ray structures are available for several cytochromes c 3 in the oxidised form (Higuchi et al, 1984;Czjzek et al, 1994;Matias et al, 1996;Simo Ä es et al, 1998). Tetrahaem cytochrome c 3 from Desulfovibrio vulgaris (Hildenborough: DvHc 3 ) is a small (14 kDa; 107 amino acid residues) soluble protein whose crystal structure in the oxidised state has been determined by X-ray diffraction (Matias et al, 1993;Simo Ä es et al, 1998).…”

“…Although the molecular basis for the ®ne regulation of several types of cooperativity mechanisms has been successfully established (Perutz, 1990), including redox-linked regulation in enzyme catalysis (Williams et al, 1997;Fu È lo È p et al, 1995;Fukuyama et al, 1995;Chen et al, 1994), no unequivocal structural basis for the cooperativity involved in electronic to protonic energy transduction has been established. This is still the case for the tetrahaem cytochromes c 3 from Desulfovibrio spp., even though considerable progress has been made in rationalising their thermodynamic properties (Santos et al, 1984;Coletta et al, 1991;Turner et al, 1994Turner et al, , 1996Park et al, 1996;Louro et al, 1996;Salgueiro et al, 1997) and high-resolution X-ray structures are available for several cytochromes c 3 in the oxidised form (Higuchi et al, 1984;Czjzek et al, 1994;Matias et al, 1996;Simo Ä es et al, 1998).…”

Crystal Structures of an Oxygen-binding Cytochrome cfrom Rhodobacter sphaeroides

“…This ligation is unlike typical class I cytochromes where the peptide carbonyl of a conserved Pro residue (Pro 30 in mitochondrial cytochrome c) provides the hydrogen bond partner for the histidine. Water as a hydrogen bonding partner to the histidine N1 has been reported for some of the heme groups in tetraheme cytochromes (28,29), and it is the hydrogen bonding partner in nitrophorin (5) and FixL (3). The imidazole aromatic plane forms a dihedral angle of 28°with the N2-Fe-N4 line in SHP, which is far from the ideal value of 45°.…”

“…The imidazole group is wedged in a hydrophobic pocket lining the proximal heme face. This pocket is formed by the side chains of residues Phe 29 . The imidazole moiety is restrained through a water-mediated hydrogen bond to the backbone oxygen atom of Ala…”