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A molecular replacement approach, augmented with the results of predictive
modeling procedures, solvent accessibility studies, packing analyses and
translational coefficient searches, has been used to elucidate the 2.8 A (1 A =
0.1 nm) resolution structure of yeast iso-1-cytochrome c. An examination of the
polypeptide chain folding of this protein shows it to have unique conformations
in three regions, upon comparison with the structures of other eukaryotic
cytochromes c. These include: residues -5 to +1 at the N-terminal end of the
polypeptide chain, which are in an extended conformation and project in large
part off the surface of the protein; residues 19 to 26, which form a surface
beta-loop on the His18 ligand side of the central heme group; and, the
C-terminal end of the helical segment composed of residues 49 to 56, which
serves to form a part of the heme pocket. Structural studies also show that the
highly reactive sulfhydryl group of Cys102 is buried within a hydrophobic region
in the monomer form of yeast iso-1-cytochrome c. Dimerization of yeast
iso-1-cytochrome c through disulfide bond formation between two such residues
would require a substantial conformational change in the C-terminal helix of
this protein. Another unique structural feature, the trimethylated side-chain of
Lys72, is located on the surface of yeast iso-1-cytochrome c near the
solvent-exposed edge of the bound heme prosthetic group. On the basis of the
results of these and other structural studies, an analysis of the spatial
conservation of structural features in the heme pocket of eukaryotic cytochromes
c has been conducted. It was found that the residues involved could be divided
into three general classes. The current structural analyses and additional
modeling studies have also been used to explain the altered functional
properties observed for mutant yeast iso-1-cytochrome c proteins.
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