Photochemical reaction center from Rhodobacter sphaeroides R-26

The photochemically active prosthetic groups (the chromophores).

1. Bacteriochlorophylls (BChl) of the special pair (red), and the ancillary pair (cyan), bacteriopheophytins (BPh) (magenta), ubiquinones (Q_A, yellow; Q_B, orange), Fe (green). The white molecule is a detergent (b-octylglucoside) which occupies the position in this carotenoid-deficient strain where the carotenoid of the reaction center sits in the wild-type (see below).

The photochemical reaction:

2. Excitation arrives at the special pair.
3. Electron transfer from the special pair likely involves participation of the ancillary BChl, but the exact role is controversial. If the reaction involves the BChl as a redox intermediate, this step has a half-time of about 3 ps, but the electron leaves with a t_½ of 0.4 ps, so no substantial accumulation of BChl^- occurs.
4. The electron arrives at BPh with a half-time of 3 ps. Charge separation is stable for a few ns
5. The electron arrives at Q_A with a half-time of 200 ps. Charge separation is stable for about 100 ms.
6. Electron transfer from Q_A to Q_B has a half-time of 30-100 µs, and is stable for about 1 s.

The protein

Hint. If the model gets too cluttered, click on this button to restore a simple view.
7. The protein as a grey wireframe model with the chromophores colored as in (1) above.
8. The protein as a spacefilling model with hydrophobic residues in white; polar residues in green, acidic residues in red and basic residues in blue. The wireframe chromophores are colored magenta. The membrane spanning part of the protein is predominantly hydrophobic; the H-subunit (top) projects into the aqueous phase on the cytoplasmic side, and has a polar surface; on the other side, the surface of the protein is at the aqueous interface on the periplasmic side (bottom), and is also polar. The acidic residues (red) on this surface are thought to provide the binding site for cytochrome c₂.
9. The protein colored by subunit, with ribbons to show secondary structure.

The remaining demonstrations will be easier to follow if you stop the rotation. Use the Chime menu (with mouse pointer on picture, click right mouse-button (or hold button down for Mac) to select Rotation, and then Stop).

The Q_B binding site

10. Zoom in on Q_B-site. Note that the L-subunit (blue) provides the protein immediately surrounding the quinone.
11. Zoom in further, and show atoms of amino acids side-chains from L-chain within 8 Å of the quinone. Atoms are CPK colored, and the red oxygens of glutamate 212, aspartate 213 and serine 223 (involved in proton relay), and the blue nitrogens of histidine 190 (ligand to proximal =O of quinone) are obvious (labels are at the C_b atoms). Ser-223 may also provide a ligand to the quinone at some stage in the catalytic cycle. In most recent structures, ser-223 is seen as H-bonded to asp-213, and the distal =O of the quinone is H-bonded to the -NH of the protein backbone at residues 224, 225.
12. Show atoms of amino acids side-chains within 8 Å of the quinone, with quinone in CPK coloring, and residues colored by type (for colors, see below). In this view, you can get a better idea of the distribution of polarity in the site. The protein lining the side of the binding pocket away from the aqueous phase is predominantly hydrophobic, and insulates the quinone from the other chromophores. The side closer to the aqueous phase is polar, and provides the apparatus for allowing H⁺ entry to the site for reduction of the quinone, and a higher dielectric for stabilization of the semiquinone anion. Notice also that the residues close to the tail are predominantly small aliphatics, providing a relatively open channel for entry and exit of the quinone.
13. Show atoms of amino acids side-chains within 8 Å of the quinone, with residues as grey space-filling models, and the quinone as an orange wireframe model. In this view, you can get a better idea of the channel for entry and exit of the quinone. (Use the mouse to rotate the model, and view down the tail.)
14. If we now show a spacefilling model of the quinone, we can see how the protein conforms to the quinone.

The Q_A binding site

15. Zoom in on Q_A-site. Note that the M-subunit (green) provides the protein immediately surrounding the quinone, and that the helical anchor of the H-subunit blocks exit.
16. Zoom in further, and show atoms of amino acids side-chains within 8 Å of Q_A. Atoms are CPK colored. Note the absence of polar residues equivalent to glu-212 and asp 213. The quinone is liganded by his-219 of the M-chain (proximal =O) and -NH of residue 260 backbone (distal =O).
17. Show atoms of amino acids side-chains within 8 Å of Q_A, with residues colored by type (for colors, see below). In this view, you can get a better idea of the distribution of polarity in the site. The protein lining the binding pocket is predominantly hydrophobic, but a tryptophan provides a "connection" to the "active" BPh. Non-polar residues insulate the quinone from the aqueous phase. Notice also that several tryptophan and phenylalanine residues close to the tail lock the quinone into its binding site.
18. Show atoms of amino acids side-chains within 8 Å of the quinone, with residues as grey space-filling models, and the quinone as a yellow wireframe model. In this view, you can get a better idea of the constraints for entry and exit of the quinone. (Use the mouse to rotate the model, and view down the tail.)
19. If we now show a spacefilling model of the quinone, we can see how the protein conforms to the quinone.

Reaction center from Rhodobacter sphaeroides wild-type

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The structure is more highly refined than that in 4rc4.pdb, with bound water molecules, here identified by their O-atoms. The most interesting features are the changed configuration of the Q_B-site to accomodate what the authors suggest might be a quinol, and the well defined channel of water molecules connecting the Q_B-site to the aqueous phase. The occupant of the Q_B-site is under some discussion. In the Ermler et al. paper (2), the authors noted that the position of the occupant of the Q_B-site was markedly different from than that seen in previous structures; they suggested that it might be a quinol. The position of the quinol or quinone is 4.5 Å further away from the iron than the position identified previously, suggesting that it has been "caught in the act" of leaving/arriving at the Q_B-site. More recently, Stowell et al. (3) have studied the structure in both dark-adapted and illuminated crystals at high resolution, and have suggested that the species at the Q_B-site seen in their dark-adapted crystals is the same as that seen by Ermler et al. (2), and is the quinone. They suggest that in all other previous structures, the occupant of the Q_B-site has been the semiquinone, formed under weak illumination, since the occupant seen in their illuminated crystals is in that position, and is likely the semiquinone generated on the single turn-over of the photochemistry which can occur when no donors are present to rereduce the P⁺ formed on illumination. Click here to view an animation of the changes at the Q_B-site between the two structures studied by Stowell et al. (3).

Chromophores are colored as follows: (BChl)₂ (the "special pair"), red; ancillary BChls, cyan or blue; Bphs, magenta or purple (lighter chromophores are active side (L-subunit)); Q_A, yellow; Q_B, orange; Fe, red; spheroidene (carotenoid), white. Waters are colored green.

The structure can best be explored using the Menu options. Before going on, Stop the Rotation, and use the mouse to manipulate the model to get a good view. Try using Slab Mode to slice through the structure, and see the water channels. Use the stereo option if you've mastered the art of crossed-eye viewing

The Q_B-site with QH₂ (?) in occupancy

1. Zoom in on the Q_B-site, to see the occupant of the Q_B-site (orange), residues his-190, glu-212, asp-213, ser-223 (colored by amino acid type), and the water chain (spacefilling O-atoms colored green).
2. Zoom in on the Q_B-site, to see the water channel in relation to the site. Quinol/quinone (orange), residues with H-bonds to waters in the channel (his-L190, arg-L207, asp-L210, glu-L212, asp-L213, ser-L223, glu-M232, arg-M233, glu-M234, leu-M235, glu-M236, asp-M240, arg-H70, arg-H117, arg-H118, glu-H122, lys-H130, asp-H170, glu-H173, arg-H177, glu-H230, - colored by amino acid type), and the water chain (spacefilling O-atoms colored green). Other waters are shown as smaller yellow spheres. (Note: the residue numbers for chains M and H differ from those published (2), which did not correspond to the PDB file.)

ASP, GLU        bright red
LYS, ARG        blue    
HIS             pale blue
ASN, GLN        cyan    
PRO             flesh   
CYS, MET        yellow  
SER, THR        orange  
GLY             light grey
TRP             pink    
PHE, TYR        mid blue
ALA             dark grey
LEU, VAL, ILE   green

1. G. Feher, J.P. Allen, M.Y. Okamura, D.C. Rees (1989) Nature 339, 111
2. U. Ermler, G. Fritzsch, S.K. Buchanan, H. Michel (1994) Structure of the photosynthetic reaction center from Rhodobacter sphaeroides at 2.65 resolution. Structure (London) 2, 925.
3. Stowell, M. H. B., McPhillips, T. M., Rees, D. C., Soltis, S. M., Abresch, E. and Feher, G. (1997) Light-Induced Structural Changes in Photosynthetic Reaction Center: Implications for Mechanism of Electron-Proton Transfer. Science, 276, 812-815