Cytochrome domain structure

The characterisation of the complexation between flavocytochrome b2 and cytochrome c has been the subject of many studies (see for example Short et al., 1998 Daff et al., 1996b and CapeillEre-Blandin, 1995). Work on the anomala flavocytochrome b2, for which there is no crystal structure, led to the conclusions that the cytochrome c binding site involved both the flavodehydrogenase and cytochrome domains (CapeillEre-Blandin and Albani, 1987) and that the complex was stabilised by electrostatic interactions (CapeillEre-Blandin, 1982). It is clear that similar conclusions hold true for the S. cerevisiae enzyme (Daff et al., 1996b) for which the crystal... 

Cytochrome c, is an amphiphilic protein with a molecular weight of 28-31000. Weiss et al. [212] found that it may be isolated only with the help of a detergent. However, by mild proteolysis they could release the haem-binding domain from the rest of the protein. This segment is soluble in aqueous solutions. The amino acid sequence of the bovine protein [181] shows that it has only one continuous hydrophobic segment that is close to the C-terminus. This segment probably acts as an anchor to the membrane. The covalently bound haem is located in the water-soluble part, with its plane perpendicular to the membrane plane [206], The two-domain structure makes the architecture of cytochrome c, very similar to that of microsomal cytochrome [213]. 

Labeyrie et al. (41) isolated a trypsin fragment of 11 kDa from S. cerevisiae flavocytochrome 62 that contained heme but was devoid of flavin and had no lactate dehydrogenase activity. The fragment, which was referred to as cytochrome 62 core, was found to have spectral properties very like those of microsomal cytochrome 65 (41). This similarity with cytochrome 65 is borne out by comparisons of amino acid sequence (42-44). The sequence similarity extends to related heme domains of sulfite oxidase (45, 46) and assimilatory nitrate reductase (47). The existence of a protein family with a common cytochrome 65 fold was suggested by Guiard and Lederer (48) and this is supported by the close similarity between the three-dimensional structures of microsomal cytochrome 65 (49) and the cytochrome domain of flavocytochrome 62 (23-25). 

The cytochrome 62 core has been shown by amino acid sequence determination to be located at the N-terminus of the flavocytochrome 62 polypeptide chain (43). It is clearly seen as a distinct domain in the crystal structure, in close contact with the much larger FMN-contain-ing domain (23-25) (Fig. 5). The cytochrome domain consists of resi-... 

The two-domain, structural motif in FNR represents a common structural feature in a large class of enzymes that catalyze electron transfer between a nicotinamide dinucleotide molecule and a one-electron carrier. Beside the photosynthetic electron-transfer enzyme, others non-photosynthetic ones include flavodoxin reductase, sulfite reductase, nitrate reductase, cytochrome reductase, and NADPH-cyto-chrome P450 reductase. FNR belongs to the group of so-called dehydrogenases-electron transferases, i.e., flavoproteins that catalyze electron transfer from two, one-electron donor molecules to a single two-electron acceptor molecule. 

Unlike DAAO, the crystal structure of F 2 does not clarify the mechanism of flavin reduction. The monomer of F 2 has a small N-terminal cytochrome domain and a larger C-terminal a/(3 barrel containing FMN, connected by a short linker. The carboxylate of the product makes a salt bridge and a hydrogen bond to an Arg and a Tyr (Figure 3), residues also present in DAAO. Unlike in DAAO, the product in the crystal structure interacts with both Tyr254 and His373, either of which could be the active site base needed in a carbanion mechanism. " The substrate, lactate, has been modeled into the structure in two different conformations. ... 

Actual and predicted structures of an (X-helical domain of cytochrome bgg2... 

FIGURE 21.11 The structure of UQ-cyt c reductase, also known as the cytochrome hci complex. The alpha helices of cytochrome b (pale green) define the transmembrane domain of the protein. The bottom of the structure as shown extends approximately 75 A into the mitochondrial matrix, and die top of the structure as shown extends about 38 A into the intermembrane space. (Photograph kindly provided by Di Xia and Johann Deismhofer [From Xia, D., Yn, C.-A., Kim, H., Xia,J-Z., Kachnrin, A. M., Zhang, L., Yn,... 

The structure of the UQ-cyt c reductase, also known as the cytochrome bc complex, has been determined by Johann Deisenhofer and his colleagues. (Deisenhofer was a co-recipient of the Nobel Prize in Chemistry for his work on the structure of a photosynthetic reaction center [see Chapter 22]). The complex is a dimer, with each monomer consisting of 11 protein subunits and 2165 amino acid residues (monomer mass, 248 kD). The dimeric structure is pear-shaped and consists of a large domain that extends 75 A into the mito-... 

Fig. 8. (a) Structure of the full-length Rieske protein from bovine heart mitochondrial bci complex. The catalytic domain is connected to the transmembrane helix by a flexible linker, (b) Superposition of the three positional states of the catalytic domain of the Rieske protein observed in different crystal forms. The ci state is shown in white, the intermediate state in gray, and the b state in black. Cytochrome b consists of eight transmembrane helices and contains two heme centers, heme and Sh-Cytochrome c i has a water-soluble catalytic domain containing heme c i and is anchored by a C-terminal transmembrane helix. The heme groups are shown as wireframes, the iron atoms as well as the Rieske cluster in the three states as space-filling representations. 

Fig. 71. Examples of protein domains with different numbers of layers of backbone structure (a) two-layer cytochrome c (b) three-layer phosphoglycerate kinase domain 2 (c) four-layer triosephosphate isomerase. The arrows above each drawing point to the backbone layers.

Fig. 105. Examples of small disulfide-rich or metal-rich proteins (shown on the right side) compared with their more regular counterparts in other structural categories (shown at the left), (a) Tobacco mosaic virus protein, an up-and-down helix bundle (b) cytochrome bs, a distorted up-and-down helix bundle (c) trypsin domain 1, a Greek key antiparallel /3 barrel (d) high-potential iron protein, a distorted Greek key /3 barrel (e) glutathione reductase domain 3, an open-face sandwich fi sheet (f) ferredoxin, a distorted open-face sandwich f) sheet.

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