Gene Cluster of Rhodothermus marinus High-Potential Iron-Sulfur Protein:Oxygen Oxidoreductase, a caa ₃ -Type Oxidase Belonging to the Superfamily of Heme-Copper Oxidases

Abstract

The respiratory chain of the thermohalophilic bacterium Rhodothermus marinus contains an oxygen reductase, which uses HiPIP (high potential iron-sulfur protein) as an electron donor. The structural genes encoding the four subunits of this HiPIP:oxygen oxidoreductase were cloned and sequenced. The genes for subunits II, I, III, and IV (named rcoxA to rcoxD) are found in this order and seemed to be organized in an operon of at least five genes with a terminator structure a few nucleotides downstream of rcoxD. Examination of the amino acid sequence of the Rcox subunits shows that the subunits of the R. marinus enzyme have homology to the corresponding subunits of oxidases belonging to the superfamily of heme-copper oxidases. RcoxB has the conserved histidines involved in binding the binuclear center and the low-spin heme. All of the residues proposed to be involved in proton transfer channels are conserved, with the exception of the key glutamate residue of the D-channel (E 278 , Paracoccus denitrificans numbering). Analysis of the homology-derived structural model of subunit I shows that the phenol group of a tyrosine (Y) residue and the hydroxyl group of the following serine (S) may functionally substitute the glutamate carboxyl in proton transfer. RcoxA has an additional sequence for heme C binding, after the Cu A domain, that is characteristic of caa 3 oxidases belonging to the superfamily. Homology modeling of the structure of this cytochrome domain of subunit II shows no marked electrostatic character, especially around the heme edge region, suggesting that the interaction with a redox partner is not of an electrostatic nature. This observation is analyzed in relation to the electron donor for this caa 3 oxidase, the HiPIP. In conclusion, it is shown that an oxidase, which uses an iron-sulfur protein as an electron donor, is structurally related to the caa 3 class of heme-copper cytochrome c oxidases. The data are discussed in the framework of the evolution of oxidases within the superfamily of heme-copper oxidases.

c -Type Cytochromes in Pelobacter carbinolicus

“…The gene encoding cytoplasmic membrane-bound monoheme cytochrome c, PCAR2549, is immediately upstream of PCAR2550, but this cytochrome has no significant similarity to other proteins. 3 -type cytochrome c oxidase (encoded by PCAR2526 to PCAR2529), which is homologous to the oxidases in other members of the Geobacteraceae, as well as the characterized oxidase in Rhodothermus marinus (42). G. sulfurreducens has a cytochrome c oxidase (36) and has been shown to grow with low levels of oxygen as a terminal electron acceptor (27).…”

Structure at 1.3Å Resolution of Rhodothermus marinus caa3 Cytochrome c Domain

“…But an electrostatic surface potential map calculated for the homology model derived for the subunit II of the R. marinus-caa 3 HiPIP:oxygen oxidoreductase has been reported. 11 A large negatively charged region can be seen at the interacting surface, as shown in Figure 4(c). This suggests that the remaining part of subunit II, the CuA, could interact with the positively charged lysine and arginine patch in the soluble domain by electrostatic complementarity.…”

“…11 Therefore, it can be proposed that the interaction of the cytochrome c domain of caa 3 HiPIP:oxygen oxidoreductase with its redox partner is hydrophobic in nature. Of course, further studies are necessary to fully understand the nature of the interaction between the cytochrome domain and its electron donor.…”

“…The caa 3 HiPIP:oxygen oxidoreductase from Rhodothermus marinus is one example of a heme-copper-containing terminal oxidase, which belongs to the A2 family, as indicated by the presence of a YS sequence motif in its subunit I D-pathway, containing in its subunit II a Cu A centre and a C-type heme. 10,11 In spite of this modification in the D-pathway, namely the absence of a glutamate residue (E278 in the case of Paracoccus denitrificans) present in A-type terminal oxidases, these enzymes are canonical proton pumps. 12,13 Furthermore, A2 enzymes are not specifically related to thermophily or to particular phylogenetic groups.…”

Structure of caa 3 cytochrome c oxidase – a nature-made enzyme-substrate complex

“…There are also reports of subunits IV in Bacillus PS3 caa 3 oxidase (Kirken et al , 1995 ), B. subtilis QOX (Santana et al , 1992 ) as well as Rh. marinus caa 3 -type HiPIP oxidase (Santana et al , 2001 ), all with three predicted TMH. None of these subunits align well with the sequence of T. thermophilus subunit IV.…”