RuBisCO
Ribulose-1,5-bisphosphate carboxylase/oxygenase, commonly known by the abbreviations RuBisCo, rubisco, RuBPCase, or RuBPco, is an enzyme involved in the light-independent part of photosynthesis, including the carbon fixation by which atmospheric carbon dioxide is converted by plants and other photosynthetic organisms to energy-rich molecules such as glucose. It emerged approximately four billion years ago in primordial metabolism prior to the presence of oxygen on Earth. It is probably the most abundant enzyme on Earth. In chemical terms, it catalyzes the carboxylation of ribulose-1,5-bisphosphate.
Alternative carbon fixation pathways
RuBisCO is important biologically because it catalyzes the primary chemical reaction by which inorganic carbon enters the biosphere. While many autotrophic bacteria and archaea fix carbon via the reductive acetyl CoA pathway, the 3-hydroxypropionate cycle, or the reverse Krebs cycle, these pathways are relatively small contributors to global carbon fixation compared to that catalyzed by RuBisCO. Phosphoenolpyruvate carboxylase, unlike RuBisCO, only temporarily fixes carbon. Reflecting its importance, RuBisCO is the most abundant protein in leaves, accounting for 50% of soluble leaf protein in plants and 30% of soluble leaf protein in plants. Given its important role in the biosphere, the genetic engineering of RuBisCO in crops is of continuing interest.Structure
In plants, algae, cyanobacteria, and phototrophic and chemoautotrophic Pseudomonadota, the enzyme usually consists of two types of protein subunit, called the large chain and the small chain. The large-chain gene is encoded by the chloroplast DNA in plants. There are typically several related small-chain genes in the nucleus of plant cells, and the small chains are imported to the stromal compartment of chloroplasts from the cytosol by crossing the outer chloroplast membrane. The enzymatically active substrate binding sites are located in the large chains that form dimers in which amino acids from each large chain contribute to the binding sites. A total of eight large chains and eight small chains assemble into a larger complex of about 540,000 Da. In some Pseudomonadota and dinoflagellates, enzymes consisting of only large subunits have been found.Magnesium ions are needed for enzymatic activity. Correct positioning of in the active site of the enzyme involves addition of an "activating" carbon dioxide molecule to a lysine in the active site. operates by driving deprotonation of the Lys210 residue, causing the Lys residue to rotate by 120 degrees to the trans conformer, decreasing the distance between the nitrogen of Lys and the carbon of. The close proximity allows for the formation of a covalent bond, resulting in the carbamate. is first enabled to bind to the active site by the rotation of His335 to an alternate conformation. is then coordinated by the His residues of the active site, and is partially neutralized by the coordination of three water molecules and their conversion to −OH. This coordination results in an unstable complex, but produces a favorable environment for the binding of. Formation of the carbamate is favored by an alkaline pH. The pH and the concentration of magnesium ions in the fluid compartment increases in the light. The role of changing pH and magnesium ion levels in the regulation of RuBisCO enzyme activity is discussed [|below]. Once the carbamate is formed, His335 finalizes the activation by returning to its initial position through thermal fluctuation.
Enzymatic activity
RuBisCO is one of many enzymes in the Calvin cycle. When RuBisCO facilitates the attack of at the C2 carbon of RuBP and subsequent bond cleavage between the C3 and C2 carbon, 2 molecules of glycerate-3-phosphate are formed. The conversion involves these steps: enolisation, carboxylation, hydration, C-C bond cleavage, and protonation.Substrates
s for RuBisCO are ribulose-1,5-bisphosphate and carbon dioxide. RuBisCO also catalyses a reaction of ribulose-1,5-bisphosphate and molecular oxygen instead of carbon dioxide.Discriminating between the substrates and O2 is attributed to the differing interactions of the substrate's quadrupole moments and a high electrostatic field gradient. This gradient is established by the dimer form of the minimally active RuBisCO, which with its two components provides a combination of oppositely charged domains required for the enzyme's interaction with O2 and. These conditions help explain the low turnover rate found in RuBisCO: In order to increase the strength of the electric field necessary for sufficient interaction with the substrates' quadrupole moments, the C- and N- terminal segments of the enzyme must be closed off, allowing the active site to be isolated from the solvent and lowering the dielectric constant. This isolation has a significant entropic cost, and results in the poor turnover rate.
Binding RuBP
Carbamylation of the ε-amino group of Lys210 is stabilized by coordination with the. This reaction involves binding of the carboxylate termini of Asp203 and Glu204 to the ion. The substrate RuBP binds displacing two of the three aquo ligands.Enolisation
of RuBP is the conversion of the keto tautomer of RuBP to an enediol. Enolisation is initiated by deprotonation at C3. The enzyme base in this step has been debated, but the steric constraints observed in crystal structures have made Lys210 the most likely candidate. Specifically, the carbamate oxygen on Lys210 that is not coordinated with the Mg ion deprotonates the C3 carbon of RuBP to form a 2,3-enediolate.Carboxylation
Carboxylation of the 2,3-enediolate results in the intermediate 3-keto-2-carboxyarabinitol-1,5-bisphosphate and Lys334 is positioned to facilitate the addition of the substrate as it replaces the third -coordinated water molecule and add directly to the enediol. No Michaelis complex is formed in this process. Hydration of this ketone results in an additional hydroxy group on C3, forming a gem-diol intermediate. Carboxylation and hydration have been proposed as either a single concerted step or as two sequential steps. Concerted mechanism is supported by the proximity of the water molecule to C3 of RuBP in multiple crystal structures. Within the spinach structure, other residues are well placed to aid in the hydration step as they are within hydrogen bonding distance of the water molecule.C-C bond cleavage
The gem-diol intermediate cleaves at the C2-C3 bond to form one molecule of glycerate-3-phosphate and a negatively charged carboxylate. Stereo specific protonation of C2 of this carbanion results in another molecule of glycerate-3-phosphate. This step is thought to be facilitated by Lys175 or potentially the carbamylated Lys210.Products
When carbon dioxide is the substrate, the product of the carboxylase reaction is an unstable six-carbon phosphorylated intermediate known as 3-keto-2-carboxyarabinitol-1,5-bisphosphate, which decays rapidly into two molecules of glycerate-3-phosphate. This product, also known as 3-phosphoglycerate, can be used to produce larger molecules such as glucose.When molecular oxygen is the substrate, the products of the oxygenase reaction are phosphoglycolate and 3-phosphoglycerate. Phosphoglycolate is recycled through a sequence of reactions called photorespiration, which involves enzymes and cytochromes located in the mitochondria and peroxisomes. In this process, two molecules of phosphoglycolate are converted to one molecule of carbon dioxide and one molecule of 3-phosphoglycerate, which can reenter the Calvin cycle. Some of the phosphoglycolate entering this pathway can be retained by plants to produce other molecules such as glycine. At ambient levels of carbon dioxide and oxygen, the ratio of the reactions is about 4 to 1, which results in a net carbon dioxide fixation of only 3.5. Thus, the inability of the enzyme to prevent the reaction with oxygen greatly reduces the photosynthetic capacity of many plants. Some plants, many algae, and photosynthetic bacteria have overcome this limitation by devising means to increase the concentration of carbon dioxide around the enzyme, including carbon fixation, crassulacean acid metabolism, and the use of pyrenoid.
Rubisco side activities can lead to useless or inhibitory by-products. Important inhibitory by-products include xylulose 1,5-bisphosphate and glycero-2,3-pentodiulose 1,5-bisphosphate, both caused by "misfires" halfway in the enolisation-carboxylation reaction. In higher plants, this process causes RuBisCO self-inhibition, which can be triggered by saturating and RuBP concentrations and solved by Rubisco activase.
Rate of enzymatic activity
Some enzymes can carry out thousands of chemical reactions each second. However, RuBisCO is slow, fixing only 3–10 carbon dioxide molecules each second per molecule of enzyme. The reaction catalyzed by RuBisCO is, thus, the primary rate-limiting factor of the Calvin cycle during the day. Nevertheless, under most conditions, and when light is not otherwise limiting photosynthesis, the speed of RuBisCO responds positively to increasing carbon dioxide concentration.RuBisCO is usually only active during the day, as ribulose 1,5-bisphosphate is not regenerated in the dark. This is due to the regulation of several other enzymes in the Calvin cycle. In addition, the activity of RuBisCO is coordinated with that of the other enzymes of the Calvin cycle in several other ways: