Structure analysis of cytochrome c3 from Desulfovibrio vulgaris Hildenborough at 1.9 A resolution.

The three-dimensional X-ray structure of cytochrome c3 from sulfate-reducing bacteria Desulfovibrio vulgaris Hildenborough (DvH) (M(r) 13 kDa, 107 residues, 4 heme groups) has been determined at 1.9 A resolution, by the method of molecular replacement, using the homologous part of the refined structure of cytochrome c3 from D. vulgaris Miyazaki F (DvMF). Crystals of c3 DvH were obtained with space group P61, a = 77.0 A, c = 77.2 A, Z = 12, corresponding to two independent molecules in the asymmetric unit. The structure was refined to an R-factor of 19.6%. The structures of the two molecules are analyzed, compared with each other and also with that of c3 DvMF. The main-chain atoms are, for the three structures, generally within 1.0 A. The intramolecular heme edge to edge distances and interplanar angles indicate two groups of values. Shorter distances are associated with near-normal angles, while longer distances with acute angles. Moreover, two of the four hemes, II and IV, are close to only one other heme, while the remaining two hemes, I and III, have two close neighbors each. The two histidine residues that co-ordinate the heme irons on the fifth and sixth positions are nearly parallel, except in the case of heme II. The only substitution from DvMF which is inside the molecule, A68V, occurs in the vicinity of that same heme. However, the non-paralellism between the two flanking histidine residues was also observed in DvMF. Heme II has a conserved higher exposure to solvent and one of the lowest redox potentials in the fully oxidized forms of the two cytochromes. A comparison between data obtained by spectroscopic techniques, nuclear magnetic resonance and electron paramagnetic resonance, and the structural results presented here, indicates two types of interactions, between hemes I and II and between hemes III and IV.