Biophysical analysis of the structural evolution of substrate specificity in RuBisCO

Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is the most abundant enzyme on Earth. However, its catalytic rate per molecule of protein is extremely slow and the binding of the primary substrate, CO<jats:sub>2</jats:sub>, is competitively displaced by O<jats:sub>2.</jats:sub> Hence, carbon fixation by RuBisCO is highly inefficient; indeed, in higher C3 plants, about 30% of the time the enzyme mistakes CO<jats:sub>2</jats:sub> for O<jats:sub>2</jats:sub>. Using genomic and structural analysis, we identify regions around the catalytic site that play key roles in discriminating between CO<jats:sub>2</jats:sub> and O<jats:sub>2</jats:sub>. Our analysis identified positively charged cavities directly around the active site, which are expanded as the enzyme evolved with higher substrate specificity. The residues that extend these cavities have recently been under selective pressure, indicating that larger charged pockets are a feature of modern RuBisCOs, enabling greater specificity for CO<jats:sub>2</jats:sub>. This paper identifies a key structural feature that enabled the enzyme to evolve improved CO<jats:sub>2</jats:sub> sequestration in an oxygen-rich atmosphere and may guide the engineering of more efficient RuBisCOs.