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 Q H 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.