In plants, algae, cyanobacteria, and phototrophic and chemoautotrophic Pseudomonadota (formerly proteobacteria), the enzyme usually consists of two types of protein subunit, called the large chain (L, about 55,000 Da) and the small chain (S, about 13,000 Da). The large-chain gene (rbcL) 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 (ribulose 1,5-bisphosphate) 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 (= four dimers) 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 (Carbon dioxide|) to a lysine in the active site (forming a carbamate).  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 (His300, His302, His335), 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 (in plants, the stroma of the chloroplast) 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.