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

Abstract Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is the key enzyme to assimilate CO2 into the biosphere. The nonredundant structural data sets for three RuBisCO domain superfamilies, i.e. large subunit C-terminal domain (LSC), large subunit N-terminal domain (LSN) and small subunit domain (SS), were selected using QR factorization based on the structural alignment with QH as the similarity measure. The structural phylogenies were then constructed to investigate a possible functional significance of the evolutionary diversification. The LSC could have occurred in both bacteria and archaea, and has evolved towards increased complexity in both bacteria and eukaryotes with a 4-helix–2-helix–2-helix bundle being extended into a 5-helix–3-helix–3-helix one at the LSC carboxyl-terminus. The structural variations of LSN could have originated not only in bacteria with a short coil, but also in eukaryotes with a long one. Meanwhile, the SS dendrogram can be contributed to the structural variations at the βA–βB-loop region. All the structural variations observed in the coil regions have influence on catalytic performance or CO2/O2 selectivities of RuBisCOs from different species. Such findings provide insights on RuBisCO improvements.