J. Morais et al., STRUCTURE OF THE TETRAHEME CYTOCHROME FROM DESULFOVIBRIO-DESULFURICANS ATCC-27774 - X-RAY-DIFFRACTION AND ELECTRON-PARAMAGNETIC-RESONANCE STUDIES, Biochemistry, 34(39), 1995, pp. 12830-12841
The three-dimensional X-ray structure of-cytochrome cs from a sulfate
reducing bacterium, Desulfovibrio desulfuricans ATCC 27774 (107 residu
es, 4 heme groups), has been determined by the method of molecular rep
lacement [Frazao et al. (1993) Acta Crystallogr. D50, 233-236] and ref
ined at 1.75 Angstrom to an R-factor of 17.8%. When compared with the
homologous proteins isolated from Desulfovibrio gigas, Desulfovibrio v
ulgaris Hildenborough, Desulfovibrio vulgaris Miyazaki F, and Desulfom
icrobium baculatus, the general outlines of the structure are essentia
ly kept [heme-heme distances, heme-heme angles, His-His (axial heme li
gands) dihedral angles, and the geometry of the conserved aromatic res
idues]. The three-dimensional structure of D. desulfuricans ATCC 27774
cytochrome c(3)Dd was modeled on the basis of the crystal structures
available and amino acid sequence comparisons within this homologous f
amily of multiheme cytochromes [Palma et al. (1994) Biochemistry 33, 6
391-6407]. This model is compared with the refined crystal structure n
ow reported, in order to discuss the validity of structure prediction
methods and critically evaluate the steps used to predict protein stru
ctures by homology modeling. The four heme midpoint redox potentials w
ere determined by using deconvoluted electron paramagnetic resonance (
EPR) redox titrations. Structural criteria (electrostatic potentials,
heme ligand orientation, EPR g values, heme exposure, data from protei
n-protein interaction studies) are invoked to assign the redox potenti
als corresponding to each specific heme in the three-dimensional struc
ture.