Heme cofactors

Sulfite oxidase is a dimetallic enzyme that mediates the two-electron oxidation of sulfite by the one-electron reduction of cytochrome c. This reaction is physiologically essential as the terminal step in oxidative degradation of sulfur compounds. The enzyme contains a heme cofactor in the 10 kDa N-terminal domain and a molybdenum center in the 42 kDa C-terminal domain. The catalytic cycle is depicted in Fig. 9. 

The preceding discussion of cytochromes c provides most detail on eukaryotic, mitchondrial cytochromes c, a small subset of this huge superfamily. Additionally, all the cytochromes c discussed in this section envelop one heme cofactor, although many cytochromes in nature contain more than one heme cofactor. Many other redox proteins contain a cytochrome c domain—a few of these mentioned here include the cytochrome bci complex discussed in Section 7.6, cytochrome c oxidase to be discussed in Section 7.8, and cytochrome c peroxidase, discussed briefly in Section 7.7 (see especially Section 7.7.4.2). 

In contrast to the peptide systems, there exists a somewhat more robust literature on the electrochemistry of hemes in the larger protein systems that provides a wealth of insight into how proteins modulate the reduction potential of heme cofactors. A variety of groups have reported the reduction potential of various hemes in four-a-helix bimdle architectures, which is beginning to reveal the fundamental factors that control heme reduction potentials. 

Catalases catalyze the conversion of hydrogen peroxide to dioxygen and water. Two families of catalases are known, one having a heme cofactor and the second a structurally distinct family, found in thermophilic and lactic acid bacteria. The manganese enzymes contain a binuclear active site and the functional form of the enzyme cycles between the (Mn )2 and the (Mn )2 oxidation states. When isolated, the enzyme is in a mixture of oxidation states including the Mn /Mn superoxidized state and this form of the enzyme has been extensively studied using XAS, UV-visible, EPR, and ESEEM spectroscopies. Multifrequency EPR and microwave polarization studies of the (Mn )2 catalytically active enzyme from L. plantarum have also been reported. ... 

Similarly, this amphiphilic polymer micelle was also used to dismpt the complex between cytochrome c (Cc) and cytochrome c peroxidase (CcP Sandanaraj, Bayraktar et al. 2007). In this case, we found that the polymer modulates the redox properties of the protein upon binding. The polymer binding exposes the heme cofactor of the protein, which is buried in the protein and alters the coordination environment of the metal. The exposure of heme was confirmed by UV-vis, CD spectroscopy, fluorescence spectroscopy, and electrochemical kinetic smdies. The rate constant of electron transfer (fc°) increased by 3 orders of magnimde for the protein-polymer complex compared to protein alone. To establish that the polymer micelle is capable of disrupting the Cc-CcP complex, the polymer micelle was added to the preformed Cc-CcP complex. The observed for this complex was the same as that of the Cc-polymer complex, which confirms that the polymer micelle is indeed capable of disrupting the Cc-CcP complex. 

The heme cofactors of a and b cytochromes are tightly, but not covalently, bound to their associated proteins the hemes of c-type cytochromes are covalently attached through Cys residues (Fig. 19-3). As with the flavoproteins, the standard reduction potential of the heme iron atom of a cytochrome depends on its interaction with protein side chains and is therefore different for each cytochrome. The cytochromes of type a and b and some of type c are integral proteins of the inner mitochondrial membrane. One striking exception is the cytochrome c of mitochondria, a soluble protein that associates through electrostatic interactions with the outer surface of the inner membrane. We encountered cytochrome c in earlier discussions of protein structure (see Fig. 4-18). 

The monooxygenases [65-70] are characterized by the axial attachment of the heme cofactor to a thiolate functionality from a cysteine residue of the protein matrix. The binding pockets of monooxygenases are usually organized in such a way as to lead the substrate directly to the active FeO subunit of the porphyrin. This... 

Peroxidases (EC 1.11.1.7). Peroxidases are hemoproteins, produced mainly by microorganisms and plants, which catalyze oxidation of the recalcitrant nonphenolic lignin units in the presence of hydrogen peroxide (Duran and Esposito, 2000). This is possible because of the formation of a high redox potential oxo-ferryl intermediate during the reaction of the heme cofactor with H202 (Martinez et al., 2005). Dubey et al. (1998) studied the polymerization of catechol by plant peroxidases and found that the resultant polymers consisted of phenylene and oxyphenylene units (Figure 2.14). 

Fig. 3.2 Solvent access surface (colors represent electrostatic potentials) showing the main channel providing access to the heme cofactor (in yellow bars) occupying a central cavity (heme pocket) and the second narrow channel present in some peroxidases, such as manganese-oxidizing peroxidases, accessing to the heme propionates (based on the crystal structure of P. eryngii VP, PDB 2BOQ)...

Tryptophan dioxygenase has a short half-life (of the order of 2 hours) and is subject to regulation by three mechanisms saturation with its heme cofactor, hormonal induction and feedback inhibition, and repression by NAD(P). 

Saturation of Tryptophan Dioxygenase with Its Heme Cofactor... 

There is a large movement of the Rieske ISP towards the cytochrome c i, such that the Fc2 S2 cluster is moved 20 A closer to the heme cofactor. 

Perhaps the best-characterized example of this mechanism involves the synthesis of heme cofactors and their subsequent incorporation into various hemoproteins (see Iron Heme Proteins Electron Transport). Succinctly, enzyme-catalyzed reactions convert either succinyl-CoA or glutamate into 5-ammolevulinic acid. This molecule is further converted through a series of intermediates to form protoporphyrin IX, the metal-ffee cofactor, into which Fe is inserted by ferrochelatase. Analogous reactions are required for the synthesis of other tetrapyrrole macrocycles such as the cobalamins (see Cobalt Bu Enzymes Coenzymes), various types of chlorophylls, and the methanogen coenzyme F430 (containing Co, Mg, or Ni, respectively). Co- and Mg-chelatases have been described for insertion of these metals into the appropriate tetrapyrrolic ring structures. ... 

ATOM records are used to specify molecules which occur frequently in biological systems. These are called the known molecules and include amino acids, heme, cofactors, some of the unnatural amino acids used by medicinal chemists and a variety of molecules of general interest to GRID users. Here is a Protein Data Bank ATOM record ... 

---