November 2000 Molecule of the Month by David Goodsell
Keywords: ribulose bisphosphate carboxylaase/oxygenase, photorespiration, carbon fixation, photosynthesis, chloroplast
Carbon is essential to life. All of our molecular machines are built around a central scaffolding of organic carbon. Unfortunately, carbon in the earth and atmosphere is locked in highly oxidized forms, such as carbonate minerals and carbon dioxide gas. In order to be useful, this oxidized carbon must be "fixed" into more organic forms, rich in carbon-carbon bonds and decorated with hydrogen atoms. Powered by the energy of sunlight, plants perform this central task of carbon fixation.
Inside plant cells, the enzyme ribulose bisphosphate carboxylase/oxygenase (rubisco) 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
In spite of its central role, rubisco is remarkably inefficient. As enzymes go, it is painfully slow. Typical enzymes can process a thousand molecules per second, but rubisco fixes only about three carbon dioxide molecules per second. Plant
cells compensate for this slow rate by building lots of the enzyme. Chloroplasts are
filled with rubisco, which comprises half of the protein. This makes rubisco the
most plentiful single enzyme on the Earth.
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
Plants and algae build a large, complex form of rubisco (shown on the left), composed of eight copies of a large protein chain (shown in orange and yellow) and eight copies of a smaller chain (shown in blue and purple). The protein shown here is taken from spinach leaves (coordinates may be found in the PDB entry 1rcx; the tobacco enzyme may be found in 1rlc). Many enzymes form similar symmetrical complexes. Often, the interactions between the different chains are used to regulate the activity of the enzyme in the process known as allostery. Rubisco, however, seems to be rigid as a rock, with each of the active sites acting independently of one another. In fact, photosynthetic bacteria build a smaller rubisco (shown on the right, taken from PDB entry 9rub) composed of only two chains, which performs its catalytic task just as well. So, why do plants build a large complex? The answer might lie in the crowded conditions under which rubisco performs its job. By packing many chains together into a tight complex, the protein reduces the surface that must be wetted by the surrounding water. This allows more protein chains, and thus more active sites, to be packed into the same space.
Exploring the Structure
The active site of rubisco is arranged around a magnesium ion. In this picture, drawn using coordinates from PDB entry
8ruc, the magnesium ion is shown at the center in green.
Above it is a small sugar molecule that is similar to the product of the rubisco reaction, and a short stretch of the protein
chain is shown at the bottom. In reality, the rubisco protein chains completely surround these molecules but are not shown here for
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 clicking "View Structure." You will find that this structure includes only one half of the entire rubisco complex--if you are interested in looking at the whole rubisco molecule, the structure in 1rcx contains all sixteen chains.
© 2015 David Goodsell & RCSB Protein Data Bank