Structural and evolutionary relationships among RuBisCOs inferred from their large and small subunits

Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is the key enzyme to assimilate CO 2 into the biosphere. The structural and evolutionary relationships among RuBisCOs were discussed at the domain level. The nonredundant sets for three superfamilies of RuBisCO, i.e. large subunit C-terminal domain (LSC), large subunit N-terminal domain (LSN) and small subunit domain (SS) were defined using QR factorization based on the structural alignment of the RuBisCO domains with QH as the similarity measure, respectively. The results suggest: (1) the core structures of LSC, LSN and SS are well conserved and homologies; (2) the LSC could have occurred naturally in both bacteria and Achaean kingdoms, and the carboxyl-terminal structure evolves increasingly complicated in both bacteria and Eukaryotae kingdoms; (3) the structural variations, such as coil structures at 67-82 positions of LSN and the βA-βB-loop of SS, could make attribution to the CO 2 /O 2 specificity of RuBisCO from different species. Such findings provide insights on RuBisCO improvement.