Revised 2006/08/02
For more information about these molecules, see your text or find these files at the Protein Data Bank and read the file headers. View these files with Deep View.
This light-harvesting protein contains seven bacteriochlorophyll a (BChl a) molecules. The macrocyles of the BChl a molecules are roughly parallel, probably oriented to optimize the efficiency of excitation transfer through this antenna complex. The Mg2+ ions are all pentacoordinate, with the four nitrogens ligands from each macrocycle, and one additional ligand provided by the protein. Examine the BChl a molecules to determine the fifth ligand to magnesium in each case.
Use SwissPdbViewer to superimpose and compare the oxidized and reduced forms of this electron-transfer protein. Electron-transfer reactions in electron-transport chains are FAST. Does a comparison of the two forms of this protein give any clues to attributes of a fast electron-transfer protein? Look at the distribution of charged residues on the surface. Do you see any clues about the nature of sites to which plastocyanin might bind? (NOTE: 1PLC.pdb contains hydrogen atoms. For clearer comparison of the two structures, use Edit:Remove Hydrogens before proceeding.)
This is the oxidized form of the 2Fe-2S ferredoxin from the cyanobacterium Anabaena. See this Medline abstract for more information.
This protein (also from Anabaena) is the terminal electron transfer agent in photosynthesis, providing electrons to reduce NADP+ to NADPH. This model contains the FAD prosthetic group and substrate NADP.
Consult your biochemistry textbook for an introduction to this photosynthetic reaction center. Read carefully about the path of electron transfer from the bacteriochlorophyll special pair (BCL2 and BCL3 in this model) to ubiquinone (U109).
Bacteriorhopsin is a light-driven proton pump of Halobacterium halobium, a salt-loving bacterium. It is the only proton pump for which there is a detailed proposed mechanism of action. Download this DeepView project file of bacteriorhopsin models that represent the six proposed stages in the proton pumping cycle. Each proton is represented as a small plus sign (+) with a sphere of dots around it. As you blink through the models, note how each proton is transferred from group to group. At the beginning of each cycle, one proton is in the cytoplasm, at the top of the protein. At the end of a cycle, that proton has been released to the extracellular space. With each cycle of light absorption and recovery, one proton is taken up from the cytoplasm and one proton is released to the extracellular space. Each pumped proton is shown in a different color, so you can follow any color through the process.
Listed below are the 5 steps represented in this project file. They are listed not in the order of what happens to an individual proton; they are listed in the order of states beginning at the resting state in which retinal is is the all-trans form, through the excitation to 13-cis and subsequent conformational changes, and back to the resting state with all-trans retinal.
For excellent reviews of this proposed process, click HERE (brief review) and HERE (extensive review). For a very readable review on how spectroscopy has been used to characterize the various intermediates in light absorption, proton transfer, and recovery, click HERE.
Remember that no one has observed this process directly. Each bacteriorhodopsin model in this collection is the result of x-ray diffraction analysis of a crystalline bacteriorhodopsin derivative. Some derivatives are actually mutants that appear to be trapped in intermediate conformations in the pumping process. Each model possesses spectroscopic properties like the corresponding transient intermediate observed by spectroscopy during pumping.
To view this enzyme, obtain the file 8RUC from the Protein Data Bank. This is a large file (about 1.6 Mb) and will take a while to download.
The model in this file is a octomer of 4 large subunits (A, C, E, G) and 4 small subunits (I, J, K, L). The active site is complete in each large subunit, so restricting your view to subunit A will provide a look at the full active site.
The active site lies in the mouth of an alpha-beta barrel much like that of triose phosphate isomerase (a so-called TIM barrel). Color your model by secondary structure to see this feature.
At the active site you will find 2-carboxyarabinitol-1,5-bisphosphate (CABP), a which is very similar in structure to the beta-ketoacid intermediate in the rubisco reaction (an intermediate analog as opposed to a transition-state analog). CABP is complexed to Mg2+ and the carboxyl group of carbamoyl-lysine (residue KCX-201), producing a model that should be similar to the active form of rubisco during the catalytic event.
For more about the model, see this Medline abstract.