Chemistry Department University of Southern Maine
Links To Files Used In Biochemistry Class (CHY 361-363)
Be sure to read the Introduction to the Biochemistry Graphics Gallery to learn how to view these files.
Topic: Selected Biosynthetic Pathways (Including Photosynthesis)
For graphics from other topics, see Topics List.
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Molecules to Explore
For more information about these molecules, see your text or find these files with the PDB's 3DB Browser and follow links to literature abstracts in the PDB file headers. View these files with either SwissPdbViewer or RasMol.
Bacteriochlorophyll A Protein (PDB file 3BCL)
This light-harvesting protein contains seven 7bacteriochlorophyll 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.
Plastocyanin, oxidized and reduced forms
·Oxidized (Cu2+) plastocyanin (1PLC.pdb)
·Reduced (Cu+) plastocyanin (5PCY.pdb)
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.)
Ferredoxin (1FXA)
This is the oxidized form of the 2Fe-2S ferredoxin from the cyanobacterium Anabaena. See this Medline abstract for more information.
Ferredoxin-NADP+ Reductase (1QUF)
This protein (also from Anabaena) is the terminal electron transfer agent in photosynthesis, providing electrons 2e- to reduce NADP+to NADPH. This model contains the FAD prosthetic group and substrate NADP.
·Why should it not surprise you to learn that this protein uses an FAD prosthetic group? (Hint: ferredoxin is a one-electron carrier, and NADPH is a two-2e--electron carrier.)
Photosynthetic Reaction Center (Excerpt from 1PRC)
·The linked file (1prcAlph.pdb) contains only the alpha-carbon backbone and hetero groups. RasMol will show only hetero groups upon loading. Use Display: Backbone to reveal the protein chain. SwissPdbViewer will ignore the alpha carbons and show only the hetero groups (still very informative).
·Here's a RasMol script showing hetero groups in wireframe, metal ions in spacefill, and the proteins chains in various colors. With RasMol running in the directory to which files are downloaded, first download 1prcAlph.pdb, then this script.
Ribulose-1,5-bisphosphate Carboxylase (Rubisco)
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 2° 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.
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