Rubisco, the Carbon Fixer Protein
Through the Jolecule program, I chose the Rubisco protein, which is known as the carbon fixer. Rubisco is used to catalyze the first major step of carbon fixation in the Calvin Cycle. Rubisco is often referred to as the most abundant protein in the world. It goes through the Calvin cycle by undergoing photosynthesis and molecular synthesis, which is seen in all plants. Carboxylation or even oxygenation of RubP, also known as ribulose-1,5-bisphosphate, is catalyzed by the Rubisco protein with carbon dioxide or oxygen. Since carbon is “locked” in highly oxidized forms, carbon dioxide gas, oxidation with carbon will allow it to be "fixed" into organic forms. Rubisco takes carbon dioxide and attaches it to ribulose bisphosphate. Rubisco then takes the chain and shortens them into two identical phosphoglycerate pieces that each contain three carbon atoms. Rubisco produces phosphoglycerate which is then recycled to create more ribulose bisphosphate in order to continue on the process of the carbon fixing cycle.
Rubisco contains a three-dimensional structure and the protein strands coil on themselves in a Quaternary structure which makes their function possible. Rubisco is composed of eight large protein chains, which forms four dimers, as well as eight small protein chains, which assembles the small subunit. A dimer is a macromolecular complex quaternary protein structure. The active sites of Rubisco are located on the large subunits between the dimer pairs. Rubisco's catalytic properties/function relies on the large subunits of the protein. In order for this enzyme to do its job, a Mg2+ ion must be positioned in an active site and a CO2 molecule added. This CO2 then reacts to produce a 6-carbon intermediate molecule. Thus, the specific shape of each active site only allows for the binding of certain molecules which then allows rubisco to carry out its function.
Here is an overview of a version of Rubisco from a photosynthetic bacteria. It is displayed as a Quaternary structure of inter-twist alpha helices with kinks. This complex protein needs the Quaternary arrangement of the polypeptide chain in order for it to be a functional protein.
Carbon is removed from Co2 and is added into ribulose bisphosphate, a short sugar chain with five carbon atoms. Since carbon is “locked” in highly oxidized forms, it must be“fixed” into more organic forms through the oxidation with carbon. Here there are two tertiary forms of the protein which combine to display a functional protein in the form of a Quaternary structure. This zoomed in picture highlights the folds of the protein, which is displaying the various points of attraction from the secondary structure and therefore create kinks within the strands.
In order for Carbon Fixation to occur, the Mg metal ion is required for the coordinate reactions. The Mg ion is positioned in an active site.
Rubisco accepts both Carbon Dioxide and O2 as a substrate, but here Mg ions coordinate with Oxygen atoms in order to undergo Carbon Fixation. The activation site of this enzyme requires the addition and activation of Carbon Dioxide to Lysine.
