Bacterial reaction centers
The Chime tutorials below require installation of the Chime plug-in, which works best with Netscape (version 4.5).
A Chime tutorial on the the photosynthetic reaction centre from the purple bacterium Rhodopseudomonas viridis. This reaction center structure was the first membrane protein solved by X-ray crystallography at atomic resolution. The tutorial provides an excellent introduction to the basic function of the reaction center in the context of the structure.
A Chime tutorial which explores the structure of the reaction center from Rhodobacter sphaeroides. Several independent structures from this bacterium have been solved. Because the protocols for genetic engineering in Rb. sphaeroides were developed much earlier than in Rps. viridis, much of our knowledge of the role of individual residues has come from the study of modified function in mutant strains engineered with specific residue changes. Another feature of interest has been that the site through which the reaction center reduces the quinone pool has been solved with several different occupancies, so that the changes in structure associated with turn-over of the catalytic site have been revealed.
- A Chime tutorial on the structure of photosystem II from the X-ray crystallographic model from the Berlin group (1, and see PDB file 1FE1)
Photosytem II (PS II) shows sequence homology to the reaction centers from the purple photosynthetic bacteria, and, before structures became available, several labs had constructed models based on use of the bacterial structures as templates. The sequence alignments suggested that the D1 subunit of photosystem II is the homologue of the L-subunit, and D2 od the M-subunit. PS II has no homologue of the H-subunit. The models are of continuing interest because the crystallographic structures show that this hypothesis was correct, and because at the current resolution (Feb 2001), no information on side chain type or orientation is available.
- A model of the acceptor side of photosystem II, - the first structural model based on the bacterial reaction center (2). (A preliminary version was constructed by Howie Robinson before coordinates were available. He calculated the z-dimension data using trigonometry from the published stereo views of the QB-site of the Rps. viridis reaction center.)
- A Chime tutorial which explores the strucure in a model of photosystem II from Jonathan Nugent's group (3).
- A model of photosystem II from Bengt Svensson (4). In this model, the positions of the chlorophylls of the special pair have been modelled on the basis of a detailed anaylsis of spectroscopic data. The rings have been rotated so they overlap less to account for the weaker interaction energies in the P680 spectrum, as compared to the (BChl)2 spectra of the bacterial reaction centers. The orientation allows identification of putative ligands to the ring substituents.
Photosytem I and Green Sulphur bacteria
A Chime tutorial which explores the strucure of photosystem I.
"The phylogenetic heterogeneity of anoxygenic phototrophic bacteria has been revealed by 16S rRNA sequence analysis, the results of which
have led to extensive taxonomic rearrangements within previously defined taxa of phototrophs and stimulated interest in this group of organisms. Anoxygenic photosynthetic bacteria can be found within 4 of the 12 phylogenetic lineages, and in some cases are highly related to photosynthetic members of these groups. The largest number of phototrophs are found in the class Proteobacteria. Comparative phylogenetic analysis using 23S rDNA sequences generally supports the topology obtained from 16S rDNA sequences. The photosynthetic reaction centers are conserved in all photosynthetic bacteria, and are of two types. One is shared by the Proteobacteria and Chloroflexus aurantiacus and is similar to Photosystem II of cyanobacteria, while Heliobacteria and Chlorobium and relatives possess a reaction center similar to the cyanobacterial Photosystem I. These similarities are supported by sequence analysis of core reaction center peptides, but contradict phylogenies reconstructed from rRNA sequence analysis. Genome analysis by means of physical mapping has been performed for only three species of anoxygenic phototrophs. Some conservation of operon structure and gene sequence has been found within the Proteobacteria, but does not extend to other phototrophs."
(Abstract, from Stackebrandt, E, Rainey, F.A. and Ward-Rainey, N.(1996) Anoxygenic phototrophy across the phylogenetic spectrum - current understannding and future perspectives. Arch. Microbiol. 166, 211-223.)
- Zouni, A., Witt, H.-T., Jan Kern, Fromme, P., Kraus, N., Saenger, W. and Orth, P. (2001) Crystal structure of photosystem II from Synechococcus elongatus at
3.8 Å resolution. Nature 409, 739-743.
- Crofts, A.R., Robinson, H.H., Andrews, K., Van Doren, S. and Berry, E. (1987) Catalytic sites for reduction and oxidation of quinones. In "Cytochrome Systems: Molecular Biology and Bioenergetics", Papa, S., Chance, B. and Ernster, L., eds. pp. 617-624, Plenum Publ., New York.
- Ruffle, S.V., Donnelly, D., Blundell, T.L., and Nugent, J.H.A. (1993) A three-dimensional model of the photosystem II reaction center in Pisum sativum (Pea). Photosytnhesis Research (in press).
- Svensson, B. (1996) Ph. D. dissertation, University of Stockholm.
Antony Crofts, University of Illinois at Urbana-Champaign,