The Crystal Structure of Bonito (Katsuo) Ferrocytochrome c at 4 Å Resolution

Tamaichi ASHIDA, Tatzuo UEKI*, Tomitake TSUKIHARA**, Akio SUGIHARA***, Tsunehiro TAKANO and Masao KAKUDO
Institute for Protein Research, Osaka University Osaka

The crystal structure of bonito ferrocytochrome c has been studied at 4 Å resolution on the basis of two isomorphous heavy atom derivatives (K3UO2F5 and K2PtCl4). The crystal of bonito ferrocytochrome c belongs to an orthorhombic system with a space group of P212121. The unit cell dimensions are: a=57.54, b=84.71 and c= 37.74 Å. The crystal contains two kinds of molecules which are nearly equivalent to each other via the pseudo-twofold axis along the a axis.

The main structural features of bonito ferrocytochrome c molecule, such as the size and shape, the pathway of the polypeptide chain, and the orientation and the environment of the heme group, appear to be similar to those of horse ferricytochrome c, although it is suggested that the side-chain conformation at the surface of ferrocytochrome c is different from that of ferricytochrome c. The molecule is a prolate spheroid of a dimension of about 30x30x35 Å. Its heme group sits in the center of the molecule, with one corner exposed to the surroundings. In the crystal, the molecules are in close contacts with one another; usually, the residues present in the contact regions have long polar side chains.

In the crystal, the PtCl42 ion is located closely at Met 65 as in the case of horse ferricytochrome c. The reagent, K2HgI4, deteriorates the crystal structure, and it cannot be used for the structure analysis. On a difference Fourier map, however, the Hg group is located closely at Cys 17, which links the heme group to the polypeptide chain.