Cytochrome Paracoccus denitrificans

Iwata, S., Ostermeier, C., Ludwig, B., Michel, H. Structure at 2.8 A resolution of cytochrome c oxidase from Paracoccus denitrificans. Nature 376 660-669, 1995. 

Ostermeier C, Harrenga A, Ermler U, Michel H. 1997. Structure at 2.7 A resolution of the Paracoccus denitrificans two-subunit cytochrome c oxidase complexed with an antibody Ev fragment. Proc Natl Acad Sci USA 94 10547. 

The solution structures of the reduced and oxidized forms of a biologically fully active 10.5 kDa fragment of the Paracoccus denitrificans cytochrome c-552 enriched with and N isotopes were obtained. No significant... 

Page, M. D., and Fetguson, S. J. (1989). A bactetial c-type cytochrome can be translocated to the periplasm as an apoform The biosynthesis of cytochrome cd, (nitrite teductase) from Paracoccus denitrificans. Mol. Microbiol. 3, 653-661. 

Timkovich, R., Dhesi, R., Martinkus, K. J., Robertson, M. K., and Rea, T. M. (1982). Isolation of Paracoccus denitrificans cytochrome cd, Comparative kinetics and other nitrite reductases. Arch Biochem. Biophys. 215, 47-58. 

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 arrangement of the metal centers is in remarkable agreement with the structure, also reported in 1995 [49b], for another member of the superfamily of heme-copper oxidases, the cytochrome oxidase from Paracoccus denitrificans. The two structures show a strikingly similar coordination and arrangement of the five redox-active metals (the two irons and three coppers). 

The cytochrome >03 structure is composed of four subunits containing 25 membrane-spanning helices with a total molecular mass of 130 kDa (Fig. 12, see color insert). The overall protein architecture is similar to that of the other cytochrome c oxidases solved so far. In fact, cytochrome bo% can be superimposed over Paracoccus denitrificans cytochrome c oxidase (ParacoccusCOX) with an rms difference of 1.6 A for 781 Ca atoms using a distance cutoff of 3.8 A (Iwata et al., 1995). This is as expected since numerous biochemical studies have shown these enzymes to perform the same function in a similar manner. In the following section the amino acid numbering will be for cytochrome 603. 

X-ray structures of 2.8-A resolution of bovine heart cytochrome c oxidase with the metals in the fully oxidized state were reported in 1995 (Tsukihara et al., 1995). The X-ray structure of cytochrome c oxidase from Paracoccus denitrificans in the fuUy oxidized azide-bound state at 2.8-A resolution was also published in the same week (Iwata et al., 1995). The structure and location of the metal sites of the two enzymes are astonishingly similar at that resolution. Later, the resolution of the bovine enzyme structure was improved to 2.3A (Yoshikawa et al., 1998). However, resolution of the Paracoccus enzyme has been improved to 2.7-A resolution (Ostermeier et al., 1997). Recently another bacterial ba3-type oxidase at 2.3-A resolution (Soulimane et al., 2000) and Escherichia coli quinol oxidase at 3.5-A resolution were reported (Abramson et al., 2000). X-ray structures of the protein and its redox-active metal sites are discussed in terms of the bovine enzyme below. 

FCSD is a periplasmic enzyme found in a number of phototrophic bacteria, as well as in Paracoccus denitrificans, that catalyzes the oxidation of sulfide to elemental sulfur (Cusanovich et al., 1991 Wodara et al., 1997). FCSD from Chromatium vinosum is a 67kDa heterodimer consisting of a 46kDa flavoprotein subunit and a 21 kDa diheme cytochrome. The secondary electron acceptor is probably a cytochrome (Gray and Knaff, 1982). The FAD is bound covalently to the flavoprotein subunit via an 8-a-methyl(S-cysteinyl) thioether linkage. 

Alefounder, P. R., and Ferguson, S. J., 1981, A periplasmic location for methanol dehydrogenase from Paracoccus denitrificans implications for proton pumping by cytochrome aa3. Biochem. Biophys. Res. Comm. 98 778n784. 

Gray, K. A., Knaff, D. B., Husain, M., and Davidson, V. L., 1986, Measurement of the oxidation-reduction potentials of amicyanin and c-type cytochromes from Paracoccus denitrificans, FEES Lett. 207 39n242. 

Lopes, H., Pettigrew, G. W., Moura, L, and Moura, J. J. G., 1998, Electrochemical study on cytochrome c peroxidase from Paracoccus denitrificans a shifting pattern of structural and thermodynamic properties as the enzyme is activated, J. Biol. Inorg. Chem. 3 6329642. 

Moir, J. W. B., and Ferguson, S. J., 1994, Properties of a Paracoccus denitrificans mutant deleted in cytochrome C550 indicate that a copper protein can substitute for this cytochrome in electron transport to nitrite, nitric oxide and nitrous oxide. Microbiology 140 3989397. 

Schroter, T., Hatzfeld, O. M., Gemeinhardt, S., Kom, M., Friedrich, T., Ludwig, B., and Link, T. A., 1998, Mutational analysis of residues forming hydrogen bonds in the Rieske [2Fe-2S] cluster of the cytochrome bcl complex in Paracoccus denitrificans, Eur. J. Biochem. 255 100nl06. 

Amicyanin is found in methylotrophic bacteria that can use methylated amines as an energy source. The inactivation of the amicyanin gene in Paracoccus denitrificans results in complete loss of its ability to grow on methylamine, a direct indication that amicyanin is a key component of the methylamine driven electron-transfer chain. Amicyanin accepts an electron from methylamine dehydrogenase and transfers it to a c-type cytochrome (see Section 5.4.5). Currently, more than a dozen amicyanin and pseudoazurin sequences are available. 

This is a remarkable reaction because the transition metal chemistry of N2O is sparse, especially with copper. Most N2O reductases are soluble, periplasmic homodimers however, there are examples of membrane-associated enzymes. " The best characterized N2O reductases are from Paracoccus denitrificans, Pseudomonas nautica, and Pseudomonas stutzeri, and most of the information presented here is derived from experiments on these enzymes. Where comparable data are available, N2O reductases from various organisms appear to be fairly similar, with the exception of the enzyme from Wolinella succinogenes, as noted above. The crystal stractmes of N2O reductase from P. nautica and more recently from P. denitrificans show two distinct copper clusters per subunit a bis-thiolate bridged dinuclear electron-transfer site (Cua), which is analogous to the Cua site in cytochrome c oxidase see Cyanide Complexes of the Transition Metals), and a novel four-copper cluster ligated by seven histidines, the catalytic copper site (Cuz), where N2O is thought to bind and be reduced. Cuz was proposed to be a copper-histidine cluster on the basis of the presence of nine strictly conserved histidine residues, and this was supported by a H NMR study that identified two non-CuA associated resonances that were assigned as copper-histidine N-H protons. ... 

Budiman K, Kannt A, Lyubenova S, Richter OMH, Ludwig B, Michel H, MacMillan F. Tyrosine 167 the origin of the radical species observed in the reaction of cytochrome c oxidase with hydrogen peroxide in Paracoccus denitrificans. Biochemistry. 2004 43 11709-11716. 

The role of subunit III in proton translocation became more enigmatic after the demonstration [163] that the reconstituted cytochrome oxidase from Paracoccus denitrificans (which lacks the equivalent of subunit III [173]) translocates protons, albeit with an apparently lower efficiency. The proton translocation is insensitive to DCCD, which does not bind covalently to this enzyme [174]. 

Figure 3.1 Three-dimensional diagram of the cytochrome-c oxidase of Paracoccus denitrificans (left panel). Only the edge of the two porphyrins (represented with white balls and sticks) can be seen in this panel. Shown in the right panel is a more detailed view of the porphyrin-based active site, which incorporates a Cu ion (grey circle) in close proximity to the Fe center (white circle) of one of the porphyrins of the heme cofactor (source ref. [5]).

Fujiwara T, Fukumori Y (1996) Cytochrome ch-type nitric oxide reductase with cytochrome c oxidase activity from Paracoccus denitrificans ATCC 35512. J Bacteriol 176 1866-1871... 

Iwata S, Ostermeier C, Ludwig B, Michel H (1995) Structure at 2.8A resolution of cytochrome c oxidase from Paracoccus denitrificans. Nature 376 660-669 Jannasch HW, Nelson DC, Wirsen CO (1989) Massive natural occurrence of unusually large bacteria (Beggiatoa sp.) at a hydrothermal deep-sea vent site. Nature 342 834—836 Jetten MSM, de Bruijn P, Kuenen JG (1997) Hydroxylamine metabolism in Pseudomonas PB16 involvement of a novel hydroxylamine oxidoreductase. Antonie van Leeuwenhoek. 71 69-74... 

Richter O-MH, Tao J, Turba A, Ludwig B (1994) A cytochrome ba3 functions as a quinol oxidase in Paracoccus denitrificans. Purification, cloning, and sequence comparison. J Biol Chem 269 23079-23086... 

CuA-centers are found in cytochrome c oxidases and in N20-reductase [40,41]. In both enzyme classes, CuA-centers subtract electrons from an external donor and transfer them either directly to the active site or indirectly via a further redox-active center [42-44]. Until recently, knowledge concerning the structure of CuA-centers was incomplete. This situation was alleviated by the publication of the crystal-structures of cytochrome c oxidase from Paracoccus denitrificans and bovine heart in 1995 [43,44]. According to these data, CuA-centers contain [2Cu-2S] structures similar to those in [2Fe-2S]-type iron-sulfur clusters. Both sulfur ligands are donated by cysteine residues in the peptide chain and form a planar structure with the copper ions [43-45]. In both structures, an electron can be delocalized over both metal-ions. In the iron-sulfur center this effect is observed in the reduced form [FeZ5+-Fe2 5+], while in the CuA-center the delo-... 

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