Cytochrome invariant residues

The electron transport protein, cytochrome c, found in the mitochondria of all eukaryotic organisms, provides the best-studied example of homology. The polypeptide chain of cytochrome c from most species contains slightly more than 100 amino acids and has a molecular weight of about 12.5 kD. Amino acid sequencing of cytochrome c from more than 40 different species has revealed that there are 28 positions in the polypeptide chain where the same amino acid residues are always found (Figure 5.27). These invariant residues apparently serve roles crucial to the biological function of this protein, and thus substitutions of other amino acids at these positions cannot be tolerated. 

Fig. 1. Primary structures of cytochrome c itt 40 species (13 mammals, 5 birds, 2 reptiles, 1 frog, 5 fish, 1 snail, 4 insects, 5 higher plants, 4 fungi). The names of the 35 or 37 invariable residues (in cytochromes containing 104 and 112 residues, respectively) are given. The number of different amino acids found in each position is given by the height of the column.

Cytochromes c from different species contain the same heme group but may differ in the nature of the amino acid residues at various positions of the polypeptide chain. The functional importance of those segments of the protein which are invariant among different species has long been recognized (Margoliash and Schejter (71)). The NMR spectra in the reduced and oxidized forms indicate that methionine is an axial ligand in all the mammalian-type cytochromes c studied so far (McDonald et al. (79) Wuthrich (111)). 

Fig. 5-24. Schematic model of sub-unit II of cytochrome oxidase. 1 vo hydrophobic helices anchor the sub-unit to the membrane. The CuA binding site is indicated in a location outside the membrane close to the COOH-terminal end of the peptide. Invariant amino acid residues are shown. Reproduced from Holm et al. (1987).

The resemblance among cytochrome c molecules extends to the level of amino acid sequence. Because of the molecule s relatively small size and ubiquity, the amino acid sequences of cytochrome c from more than 80 widely ranging eukaryotic species were determined by direct protein sequencing by Emil Smith, Emanuel Margoliash, and others. Comparison of these sequences revealed that 26 of 104 residues have been invariant for more than one and a half billion years of evolution. A phylogenetic tree, constructed from the amino acid sequences of cytochrome c, reveals the evolutionary relationships between many animal species (Figure 18.24). 

SH3 domains occur in signal proteins that are involved in Tyr kinase signaling pathways (review Macias et al., 2002). They are also found in proteins of the cytoskeleton and in a subunit of the neutrophilic cytochrome oxidase. Ligand binding at SH3 domains takes place via Pro-rich sequences of ca. 10 amino acids. The sequence X-P-p-X-P is a consensus sequence for SH3 ligands, in which the two proline residues P are invariant X is usually an aliphatic residue and p is often a Pro residue. The structural... 

The last of the critical eight aromatic rings is phenylalanine-82, totally invariant over all 60 eukaryotic sequences and the two bacterial cytochromes whose three-dimensional structures are known. It is found nested against the heme, closing the upper left of the heme crevice as shown in Fig. 6. Although this residue was formerly believed from the two-derivative, 2.8 A resolution electron density map of horse oxidized cytochrome to be swung out and away from the heme in ferricytochrome (12-1J ), the four-derivative, 2.0 A map of tuna ferricytochrome has revealed this to be incorrect (15). In both oxidation states, phenylalanine-82 appears to lie next to the heme, and the crevice remains "closed in the sense observed in Fig. 7. 

Residue 72 is in a region which is invariant in plant and microbial cytochrome c s and residue 86 is in a region which is characterized in almost all cytochromes as being either Lys-Lys or Lys-Lys-Lys. Neurospora cytochrome c contains c-N-trimethyllysine at residue 72 only, and animal and most plant cytochrome c s are not methylated. 

Cytochrome c is a small haem protein with a molecular mass of around 12 kDa the precise value depends on the origin of the protein. Its biological function is to accept an electron at Complex III of the respiratory chain and deliver it to Complex IV, the terminal oxidase, normally cytochrome c oxidase. In yeast and some bacteria, cytochrome c peroxidase (CcP, EC 1.11.1.5) may act as an alternative electron acceptor. Cytochrome c has around 104 amino acid residues, 27 of which are known to be invariant between 50 different organisms. The protein is about 3.4 nm in diameter, and crystal structures on a number of examples from... 

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