The Overall Structure

All bacterial reaction centers contain at least two protein subunits, termed the L and M subunits, that surround the cofactors [1, 2]. These two subunits each contain five transmembrane helices that are organized around a twofold symmetry axis of the protein [3-9] (Figure 12.1a). The protein is largely composed of a helices, most notably the transmembrane helices that are composed of 24 to 31 amino acid residues with a pronounced hydrophobic character. At the center of the protein are four intertwining helices, two from each subunit, forming a four helical bundle that spans the cell membrane (Figure 12.1b). These helices can be thought of as being the core of the protein with the remaining helices as more peripheral. The cofactors that participate in electron transfer all lie within this core and are arranged in symmetry-related A and B branches. In addition to the transmembrane helices, there are several other smaller a helices. Three of these helices in each subunit are aligned on the periplasmic surface of the protein along the edge of the cell membrane. In each subunit, another helix is on the cytoplasmic side of the protein and largely forms the binding site for one of the quinone cofactors.

Reaction centers from purple bacteria have an additional subunit termed the H subunit. The H subunit has one transmembrane helix and a large extramembra-nous domain on the cytoplasmic side of the reaction center. While the H subunit

Figure 12.1 (a) Structure of the reaction helices surrounding the A (right hand side)

center from R. sphaeroides showing the three and B (left hand side) branches of cofactors protein subunits: L (yellow), M (blue), and H consisting of the bacteriochlorophyll dimer

(green) and the cofactors (red). (b) Structure (red), two bacteriochlorophyll monomers of the core motif found in photosynthetic (purple), two bacteriopheophytins (orange), complexes formed by the L (yellow) and M quinones and non-heme iron (brown).

(blue) subunits: the four central Coordinates from 4RCR.pdb [5]. transmembrane helices and six smaller

Figure 12.1 (a) Structure of the reaction helices surrounding the A (right hand side)

center from R. sphaeroides showing the three and B (left hand side) branches of cofactors protein subunits: L (yellow), M (blue), and H consisting of the bacteriochlorophyll dimer

(green) and the cofactors (red). (b) Structure (red), two bacteriochlorophyll monomers of the core motif found in photosynthetic (purple), two bacteriopheophytins (orange), complexes formed by the L (yellow) and M quinones and non-heme iron (brown).

(blue) subunits: the four central Coordinates from 4RCR.pdb [5]. transmembrane helices and six smaller does not have any direct interactions with the cofactors, its presence stabilizes the protein [10] and is required for assembly of the functional complex [11-13].

While all reaction centers from purple bacteria have three subunits, L, M, and H, the total number of subunits is either three or four. Some reaction centers, including the well- characterized species Rhodobacter sphaeroides and Rhodobacter capsulatus, have only the three subunits. However, reaction centers from many other purple bacteria, including those from Blastochloris viridis, have a bound cytochrome subunit that contains four hemes (Figure 12.2a). This subunit is located on the periplasmic side of the protein complex and forms a large globular domain. After light excites the bacteriochlorophyll dimer, an electron is transferred to the A branch bacteriopheophytin and then to the primary and secondary quinone acceptors. The presence of the tetraheme subunit near the bacteriochlorophyll dimer allows the closest heme to serve as a rapid secondary electron donor for the oxidized bacteriochlorophyll dimer.

Figure 12.2 (a) Structure of the reaction center from Blastochloris viridis showing the cofactors (red), including the four hemes (pink), and the four protein subunits: L (yellow), M (blue), H (green), and tetraheme (wheat). Coordinates from 4PRC.pdb [4]. (b) Structure of the reaction center-cytochrome c2 complex from R. sphaeroides showing the cofactors (red), including the heme (pink)

Figure 12.2 (a) Structure of the reaction center from Blastochloris viridis showing the cofactors (red), including the four hemes (pink), and the four protein subunits: L (yellow), M (blue), H (green), and tetraheme (wheat). Coordinates from 4PRC.pdb [4]. (b) Structure of the reaction center-cytochrome c2 complex from R. sphaeroides showing the cofactors (red), including the heme (pink)

and the protein subunits: L (yellow), M (blue), H (green), and the cytochrome (wheat). The binding of the cytochrome essentially leaves the structure of the reaction center unchanged, except for the amino acid side chains participating at the binding site and the amino terminus region of the M subunit. Coordinates from 1 L9B.pdb [14].

and the protein subunits: L (yellow), M (blue), H (green), and the cytochrome (wheat). The binding of the cytochrome essentially leaves the structure of the reaction center unchanged, except for the amino acid side chains participating at the binding site and the amino terminus region of the M subunit. Coordinates from 1 L9B.pdb [14].

Cyclic electron transfer is achieved through a series of subsequent electron and proton transfer processes involving the reaction center and the cytochrome fecj complex (see Chapter 7). Critical to the cyclic process is the involvement of the secondary quinone, as discussed below, and a water-soluble cytochrome c2. These two cellular components serve as electron and proton carriers between the reaction center and cytochrome bcj complex. Unlike the tetraheme subunit, the cytochrome c2 binds only transiently to the reaction center in order to perform electron transfer [15]. Once the water-soluble cytochrome c2 is bound to the reaction center, electron transfer proceeds in 1 |is. The binding of the cytochrome to the periplasmic surface of the reaction center of R. sphaeroides has been shown by protein crystallography to result in the heme residing directly over the bacteriochlorophyll dimer [ 14] (Figure 12.2b). While electrostatic interactions are the primary factors that determine the binding, other interactions such as hydrophobic interactions establish the final configuration of the bound complex [ 16] [ For bacterial reaction centers with a bound tetraheme subunit, after an electron is transferred to the oxidized bacteriochlorophyll dimer, the tetraheme is subsequently reduced by cytochrome

In contrast to the reaction centers from purple bacteria, the reaction center from the green bacterium Chloroflexus auranticus has only two subunits, corresponding to the L and M subunits [17]. The cofactors and their properties are similar to those in purple bacteria except that in place of the B-side bacteriochlorophyll monomer there is a bacteriopheophytin. The difference in protein composition reflects the more extensive light-harvesting complexes found in green bacteria. Purple bacteria have their lighLharvesting complexes located exclusively in the cell membrane. Energy transfer then occurs from the bacteriochlorophylls of the light-harvesting complex to the reaction center, all within the membrane (see Chapter 14). Green bacteria have a large light-harvesting complex termed a chlorosome that is attached to the cell membrane. The smaller size of the reaction center of green bacteria allows it to pack in the membrane close to the chlorosome, perhaps being attached to it, and to accept the captured light energy.

The L and M subunits in wild-type reaction centers encase a total of 10 cofactors. At the periplasmic side are two closely associated bacteriochlorophylls that serve as the primary electron donor. Each branch also has a bacteriochlorophyll monomer, a bacteriopheophytin, and a quinone. The single non- heme iron atom lies on the symmetry axis between the two quinones. The only cofactor that does not follow the symmetry pattern is the carotenoid that is asymmetrically positioned near one of the bacteriochlorophyll monomers. The properties of these cofactors are discussed below.

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