Structure of cytochrome f

The heme group, showing ligands

1. Heme group colored orange; Fe atom of heme and Tyr-1 and His-25 are spacefilling models colored by CPK atom type, protein as gray wireframe model. Note that one ligand for the heme is provided by the terminal -NH₂-group of tyrosine 1.

   The protein

2. The protein added as a gray wireframe model.
3. The protein as a Richardson cartoon, colored by structure (helix, pink; sheet, orange; turn, blue; coil, white).

   The buried water chain

4. The buried water chain shown with yellow spacefilling spheres for the water O-atoms. Atoms within 6 Å of the waters are also shown, and colored by amino acid type (or brown-green for waters)
5. The other waters.

   The surface

6. Cytochrome f colored to show the distribution of polarity and charge on the surface. Hydropbobic residues are white, polar residues green-blue, acidic and basic residues are red and blue respectively. The heme is orange, and the buried water chain is yellow.

   Plastocyanin has a surface patch of acidic residues thought to be of importance in docking to cytochrome f on the basis of cross-linking experiments, and mutagenesis. Look for basic patches which might provide a complementary electrostatic surface.
   Click here to see an image of the docking sites proposed.

   Click here to see an image of the plastocyanin surface color coded to show polarity.

   See ref 3 for work using site directed mutagenesis to test the hypothesis that electrostatic interaction between the sites shown is important determining the rate of cytochrome f oxidation in vivo.
   .

References

1. Cramer, W.A., Soriano, G.M., Ponamarev, M., Huang, D., Zhang, H.,Martinez, S.E. and Smith, J.L. (1996) Some new structural aspects and old controversies concerning the cytochrome b₆ complex of oxygenic photosynthesis. Ann. Rev. Plant Physiol. Plant Mol. Biol. 47, 477-508.
2. Coordinates for cytochrome f were kindly provided by Prof. Bill Cramer. This data set is at a somewhat higher resolution than that provided as 1ctm.pdb though the Brookhaven Protein Data Bank.
3. Soriano, G.M., Ponamarev, M., Tae, G.-S. and Cramer, W.A. (1996) Effects of interdomain basic regions of cytochrome f on its redoxx reactions in vivo. Biochemistry, 35, 14590-98.