Crystal Structure of Oxidized Bacillus pasteurii Cytochrome c 553 at 0.97-Å Resolution

This article reports the first X-ray structure of the soluble form of a c-type cytochrome isolated from a Gram-positive bacterium. Bacillus pasteurii cytochrome c 553, characterized by a low reduction potential and by a low sequence homology with cytochromes from Gram-negative bacteria or eukaryotes, is a useful case study for understanding the structure−function relationships for this class of electron-transfer proteins. Diffraction data on a single crystal of cytochrome c 553 were obtained using synchrotron radiation at 100 K. The structure was determined at 0.97-Å resolution using ab initio phasing and independently at 1.70 Å in an MAD experiment. In both experiments, the structure solution exploited the presence of a single Fe atom as anomalous scatterer in the protein. For the 0.97-Å data, the phasing was based on a single data set. This is the most precise structure of a heme protein to date. The crystallized cytochrome c 553 contains only 71 of the 92 residues expected from the intact protein sequence, lacking the first 21 amino acids at the N-terminus. This feature is consistent with previous evidence that this tail, responsible for anchoring the protein to the cytoplasm membrane, is easily cleaved off during the purification procedure. The heme prosthetic group in B. pasteurii cytochrome c 553 is surrounded by three α-helices in a compact arrangement. The largely exposed c-type heme group features a His−Met axial coordination of the Fe(III) ion. The protein is characterized by a very asymmetric charge distribution, with the exposed heme edge located on a surface patch devoid of net charges. A structural search of a representative set of protein structures reveals that B. pasteurii cytochrome c 553 is most similar to Pseudomonas cytochromes c 551, followed by cytochromes c 6, Desulfovibrio cytochrome c 553, cytochromes c 552 from thermophiles, and cytochromes c from eukaryotes. Notwithstanding a low sequence homology, a structure-based alignment of these cytochromes shows conservation of three helical regions, with different additional secondary structure motifs characterizing each protein. In B. pasteurii cytochrome c 553, these motifs are represented by the shortest interhelix connecting fragments observed for this group of proteins. The possible relationships between heme solvent accessibility and the electrochemical reduction potential are discussed.