Three-dimensional structures cytochrome

Figure 12.14 The three-dimensional structure of a photosynthetic reaction center of a purple bacterium was the first high-resolution structure to be obtained from a membrane-bound protein. The molecule contains four subunits L, M, H, and a cytochrome. Subunits L and M bind the photosynthetic pigments, and the cytochrome binds four heme groups. The L (yellow) and the M (red) subunits each have five transmembrane a helices A-E. The H subunit (green) has one such transmembrane helix, AH, and the cytochrome (blue) has none. Approximate membrane boundaries are shown. The photosynthetic pigments and the heme groups appear in black. (Adapted from L. Stryer, Biochemistry, 3rd ed. New York ...

This technique has been described as a general method of studying protein-protein interactions as well as a method for investigating the three-dimensional structure of individual proteins (Muller et al., 2001 Back et al., 2003 Dihazi and Sinz, 2003 Sinz, 2003 Sinz, 2006). It also has been used for the study of the interactions of cytochrome C and ribonuclease A (Pearson et al., 2002), to investigate the interaction of calmodulin with a specific peptide binder (Kalkhof et al., 2005a Schmidt et al., 2005), and for probing laminin self-interaction (Kalkhof et al., 2005b). 

As another example, the three-dimensional structure of Cytochrome c has been determined on the basis of structural information from pseudocontact paramagnetic chemical shifts, Curie-Dipolar cross-correlation, secondary structure constraints, dipolar couplings and 15N relaxation data [103]. This protein has a paramagnetic center, and therefore the above-mentioned conformational restraints can be derived from this feature. Dipolar couplings do not average to zero because of the susceptibility tensor anisotropy of the protein. The structure determination of this protein without NOE data gives an RMSD (root... 

Fig. 21.4 Three-dimensional structure of the enzyme cytochrome P450 oxidoreductase. The cofactors FAD and FMN are depicted in light blue. Loop regions are represented by cylindrical rods (yellow) a-helices and /(-sheets (in white) are represented by ribbons and arrows, respectively. Resonance assignments for the residues located in the key loops regions [30] highlighted in purple and red were obtained with a 3D SEA-HNCA-TROSY experiment.

First the structures of cytochrome cytochrome c peroxidase [21] are both known at high resolution. Although the precise three dimensional structure of the protein-protein complex is unknown (and, we shall argue, unknowable), molecular modeling has produced detailed stereochemical models for the c ccp complex which are subject to experimental testing and subsequent improvement, as detailed below. 

Figure 2. Three-dimensional structure of human cytochrome c created by Protein Adviser, ver 3.0 (FQS, Hakata, Japan) with PDB file of human cytochrome c down-loaded from protein structure database of NCBI. a-Helices are shown as purple ribbons, random coils as white strands, and P-tums are blue (see separate colour tip). Heme c is depicted in white straight lines inside the protein.

Matias PM, Coelho R, Pereira lA, et al. 1999. The primary and three-dimensional structures of a nine haem cytochrome c from Desulfovibrio desulfuricans ATCC 2111A reveal a new member of the Hmc family. Structure 7 119-30. 

Cytochromes are electron-transfer proteins having one or several haem groups. Cytochrome c binds to the protein by one or, more commonly two, thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. Cytochrome c has been proved to be a useful model system for studying the relationship between protein structure and thermostability due to the availability of its three-dimensional structure from a wide variety of organisms, both mesophiles and thermophiles. 

Now we can ask what is likely to happen to the three-dimensional structure of a protein if we make a conservative replacement of one amino acid for another in the primary structnre. A conservative replacement involves, for example, substitution of one nonpolar amino acid for another, or replacement of one charged amino acid for another. Intnitively, one would expect that conservative replacements would have rather little effect on three-dimensional protein structure. If an isoleucine is replaced by a valine or leucine, the structnral modification is modest. The side chains of all of these amino acids are hydrophobic and will be content to sit in the molecnlar interior. This expectation is borne out in practice. We have noted earlier that there are many different molecnles of cytochrome c in nature, all of which serve the same basic function and all of which have similar three-dimensional structnres. We have also noted the species specificity of insulins among mammalian species. Here too we find a number of conservative changes in the primary structure of the hormone. Although there are exceptions, as a general rule conservative changes in the primary structnre of proteins are consistent with maintenance of the three-dimensional structures of proteins and the associated biological functions. 

The oxidation/reduction of redox cofactors in biological systems is often coupled to proton binding/release either at the cofactor itself or at local amino acid residues, which provides the basic mechanochem-ical part of a proton pump such as that foimd in cytochrome c oxidase (95). Despite a thermodynamic cycle that provides that coupling of protonation of amino acids to the reduction process will result in a 60 mV/pH decrease unit in the reduction potential per proton boimd between the pAa values in the Fe(III) and Fe(II) states, the essential pumping of protons in the respiratory complexes has yet to be localized within their three-dimensional structures. 

The three-dimensional structures of the reaction centers of purple bacteria (Rhodopseudomonas viridis and Rhodobacter sphaeroides), deduced from x-ray crystallography, shed light on how phototransduction takes place in a pheophytin-quinone reaction center. The R. viridis reaction center (Fig. 19-48a) is a large protein complex containing four polypeptide subunits and 13 cofactors two pairs of bacterial chlorophylls, a pair of pheophytins, two quinones, a nonheme iron, and four hemes in the associated c-type cytochrome. 

Many cytochromes c are soluble but others are bound to membranes or to other proteins. A well-studied tetraheme protein binds to the reaction centers of many purple and green bacteria and transfers electrons to those photosynthetic centers.118 120 Cytochrome c2 plays a similar role in Rhodobacter, forming a complex of known three-dimensional structure.121 Additional cytochromes participate in both cyclic and noncyclic electron transport in photosynthetic bacteria and algae (see Chapter 23).120,122 124 Some bacterial membranes as well as those of mitochondria contain a cytochrome bct complex whose structure is shown in Fig. 18-8.125,126... 

In bacteria some cytochromes b and dt serve as terminal electron carriers able to react with 02, nitrite, or nitrate, while others act as carriers between redox systems.141-1433 The aldehyde heme a is utilized by animals and by some bacteria in cytochrome c oxidase, a complex enzyme whose three-dimensional structure is known (see Fig. 18-10) and which is discussed further in Chapter 18. 

Because the three-dimensional structures of the peroxidase, its reductant cytochrome c, and the complex of the two (Fig. 16-9) are known, cytochrome c peroxidase is the subject of much experimental study. Other fungal peroxidases, some of which contain manganese rather than iron, act to degrade lignin (Chapter 25).218 A lignin peroxidase from the white wood-rot fungus Phanerochaete chrysosporium has a surface tryptophan with a specifically hydroxylated C(3 carbon atom which may have a functional role in catalysis.2183 0... 

Thiosulfate cyanide sulfurtransferase symmetry in 78 TTiiouridine 234 Three-dimensional structures of aconitase 689 adenylate kinase 655 aldehyde oxido-reductase 891 D-amino acid oxidase 791 a-amylase, pancreatic 607 aspartate aminotransferase 57,135 catalytic intermediates 752 aspartate carbamyltransferase 348 aspartate chemoreceptor 562 bacteriophage P22 66 cadherin 408 calmodulin 317 carbonic acid anhydrase I 679 carboxypeptidase A 64 catalase 853 cholera toxin 333, 546 chymotrypsin 611 citrate synthase 702, 703 cutinase 134 cyclosporin 488 cytochrome c 847 cytochrome c peroxidase 849 dihydrofolate reductase 807 DNA 214, 223,228,229, 241 DNA complex... 

Complex IV. Cytochrome c oxidase (ubiquinol-cytochrome c oxidoreductase). Complex IV from mammalian mitochondria contains 13 subunits. All of them have been sequenced, and the three-dimensional structure of the complete complex is known (Fig. 18-10).125-127 The simpler cytochrome c oxidase from Paracoccus denitrificans is similar but consists of only three subunits. These are homologous in sequence to those of the large subunits I, II, and III of the mitochondrial complex. The three-dimensional structure of the Paracoccus complex is also known. Its basic structure is nearly identical to that of the catalytic core of subunits I, II, and III of the mitochondrial complex (Fig. 18-10,A).128 All three subunits have transmembrane helices. Subunit III seems to be structural in function, while subunits I and II contain the oxidoreductase centers two hemes a (a and a3) and two different copper centers, CuA (which contains two Cu2+) and a third Cu2+ (CuB) which exists in an EPR-silent exchange coupled pair with a3. Bound Mg2+ and Zn2+ are also present in the locations indicated in Fig. 18-10. 

The CuA center has an unusual structure.130-132 It was thought to be a single atom of copper until the three-dimensional structure revealed a dimetal center, whose structure follows. The CuB-cytochrome a3 center is also unusual. A histidine ring is covalently attached to tyrosine.133-1353 Like the tyrosine in the active site of galactose oxidase (Figs. 16-29,16-30), which carries a covalently joined cysteine, that of cytochrome oxidase may be a site of tyrosyl radical formation.135... 

Reaction centers of purple bacteria. The exact composition varies, but the properties of reaction centers from several genera of purple bacteria are similar. In Rhodopseudomonas viridis there are three peptide chains designated H, M, and L (for heavy, medium and light) with molecular masses of 33,28, and 24 kDa, respectively. Together with a 38-kDa tetraheme cytochrome (which is absent from isolated reaction centers of other species) they form a 1 1 1 1 complex. This constitutes reaction center P870. The three-dimensional structure of this entire complex has been determined to 0.23-nm resolution288 319 323 (Fig. 23-31). In addition to the 1182 amino acid residues there are four molecules of bacteriochlorophyll (BChl), two of bacteriopheophytin (BPh), a molecule of menaquinone-9, an atom of nonheme iron, and four molecules of heme in the c type cytochrome. In 1984, when the structure was determined by Deisenhofer and Michel, this was the largest and most complex object whose atomic structure had been described. It was also one of the first known structures for a membrane protein. The accomplishment spurred an enormous rush of new photosynthesis research, only a tiny fraction of which can be mentioned here. 

The reaction Fe ccp/Fe cytc + Fe ccp/Fe cytc proceeds with AE s 0.4V. The reaction h j been moj ored both by pulse radiolysis, and by simple mixing of Fe ccp + Fe1 cytc, with equivalent results k 0.25 0.07 s (figure 10) It is interesting that a dependence of rate on the primary structure of the protein is observed (at constant AG) for horse cy1j.c/ccp(yeast) k = 0.25 s but for yeast. cytc/(yeast) ccp k = 4 s 1 and for tuna cytc/yeast ccp k s 0.1 s, even though the general three dimensional structures are essentially identical for horse, tuna and yeast cytochromes c. These determinations disprove an earlier suggestion based on modulated excitation spectroscopy, that k - 10 s. Clearly the rate is slow,... 

Zvelebil MJ, Wolf CR, Sternberg MJ. A predicted three-dimensional structure of human cytochrome P450 implications for substrate specificity. Protein Eng 1991 ... 

Chang YT, Loew GH. Construction and evaluation of a three-dimensional structure of cytochrome P450choP enzyme (CYP105C1). Protein Eng 1996 9 755-766. 

Matias PM, Soares CM, Saraiva LM, Coelho R, Morals J, Le Gall J, Carrondo MA (2001) [NiFe] hydrogenase from Desulfovibrio desulfuricans ATCC 27774 gene sequencing, three-dimensional structure determination and refinement at 1.8 A and modelling studies of its interaction with the tetrahaem cytochrome. J. Biol. Inorg. Chem. 6 63-81... 

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