A detailed comparison of the refined structures of cytochrome c3 molecules from two strains in Desulfovibrio vulgaris: the relationship between the heme structures and their redox properties.
The refined structures of the cytochrome c3 molecules from Desulfovibrio vulgaris Miyazaki and Hildenborough have been compared in detail. Though there are no significant differences of the overall structure and spatial arrangement of four heme groups between two molecules, there are some unique features with regard to the local structures near the heme pockets. Two of the heme groups show significant differences including a hydrogen bonding scheme between the imidazole rings and water molecules in heme pocket. The water molecule near the heme 1 pocket in Miyazaki cytochrome c3 is replaced by the C delta 1 atom of Leu9 in the Hildenborough structure. The rotation around the C alpha-C beta bond of Leu9 results in the increase of the solvent accessibility of the portion of the heme 1 edge. On the other hand, in heme3 one water molecule is additionally included in the hydrogen bonding network with a N delta 1 atom of the imidazole ring and carbonyl oxygen atom of the main chain in Hildenborough cytochrome c3. This additional hydrogen bonding network will contribute to the possible passage between the imidazole ring and the molecular surface. These features have been related to the upfield shift of the C2 proton signals of NMR spectra and the low redox potentials of the cytochrome c3 molecules of Desulfovibrio vulgaris Hildenborough in comparison with those from Miyazaki.
Higuchi
Y
Y
Department of Life Science, Himeji Institute of Technology, Hyogo, Japan.
Akutsu
H
H
Yasuoka
N
N
D000595:Amino Acid Sequence; D003574:Cytochrome c Group / Q000737:chemistry*; D016969:Desulfovibrio vulgaris / Q000201:enzymology*; D006418:Heme / Q000737:chemistry*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010084:Oxidation-Reduction; D011487:Protein Conformation; D016415:Sequence Alignment; D012997:Solvents; D013045:Species Specificity
D003574:Cytochrome c Group; D012997:Solvents; D006418:Heme; C017165:cytochrome c(3)