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
Rubisco in Action
The active site of rubisco is centered on a magnesium ion (green). It is held tightly by three amino acids: an asparagine, glutamic acid, and a modified form of lysine. The carbon dioxide molecule (left, dotted outline) attached to this lysine serves as an activator in the carbon fixing reaction. This activator carbon dioxide is different from the carbon dioxide molecule that is fixed to the sugar. During the day, the activator carbon dioxide is attached to rubisco, and removed at night to turn the enzyme "off." When rubisco is active, the exposed side of the magnesium ion is free to bind to the sugar molecule and catalyze the reaction with a substrate carbon dioxide. In this structure (PDB ID 8ruc), the carbon dioxide is already attached to the sugar (right, dotted outline), giving a snapshot of rubisco in action.
Select the JSmol tab to explore these structures in an interactive view.
This JSmol was designed and illustrated by Ryan Nini.
November 2000, David Goodsellhttp://doi.org/10.2210/rcsb_pdb/mom_2000_11