Molecule of the Month: Rubisco
Rubisco fixes atmospheric carbon dioxide into bioavailable sugar molecules
Inside plant cells, the enzyme ribulose bisphosphate carboxylase/oxygenase (rubisco, shown here from PDB entry 1rcx ) forms the bridge between life and the lifeless, creating organic carbon from the inorganic carbon dioxide in the air. Rubisco takes carbon dioxide and attaches it to ribulose bisphosphate, a short sugar chain with five carbon atoms. Rubisco then clips the lengthened chain into two identical phosphoglycerate pieces, each with three carbon atoms. Phosphoglycerates are familiar molecules in the cell, and many pathways are available to use it. Most of the phosphoglycerate made by rubisco is recycled to build more ribulose bisphosphate, which is needed to feed the carbon-fixing cycle. But one out of every six molecules is skimmed off and used to make sucrose (table sugar) to feed the rest of the plant, or stored away in the form of starch for later use.
Slow and Steady
Rubisco also shows an embarrassing lack of specificity. Unfortunately, oxygen molecules and carbon dioxide molecules are similar in shape and chemical properties. In proteins that bind oxygen, like myoglobin, carbon dioxide is easily excluded because carbon dioxide is slightly larger. But in rubisco, an oxygen molecule can bind comfortably in the site designed to bind to carbon dioxide. Rubisco then attaches the oxygen to the sugar chain, forming a faulty oxygenated product. The plant cell must then perform a costly series of salvage reactions to correct the mistake.
Sixteen Chains in One
Exploring the Structure
The magnesium ion is held tightly by three amino acids, including a surprising modified form of lysine (the bonds between the ion and the protein are shown by the three yellow lines going downwards). An extra carbon dioxide molecule, shown in larger spheres just below the magnesium ion, is attached firmly to the end of the snaky lysine sidechain. In plant cells, this "activator" carbon dioxide, which is different from the carbon dioxide molecules that are fixed in the reaction, is attached to rubisco during the day, turning the enzyme "on," and removed at night, turning the enzyme "off." The exposed side of the magnesium ion is then free to bind to both ribulose bisphosphate, holding onto two oxygen atoms (small red spheres), and the carbon dioxide molecule that will be attached to sugar. In this structure, the carbon dioxide, shown with larger spheres above the magnesium ion, is already attached to the sugar.
This illustration was created with RasMol. You can create similar illustrations by going to entry 8ruc and choose one of the options for 3D viewing. You will find that the asymmetric unit of this structure includes only one half of the entire rubisco complex, so be sure to view the biological assembly. Or, you can explore the structure in 1rcx , which contains all sixteen chains.
November 2000, David Goodselldoi:10.2210/rcsb_pdb/mom_2000_11