Structural and functional analyses of Rubisco from arctic diatom species reveal unusual posttranslational modifications

J Biol Chem. 2018 Aug 24;293(34):13033-13043. doi: 10.1074/jbc.RA118.003518. Epub 2018 Jun 20.


The catalytic performance of the major CO2-assimilating enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), restricts photosynthetic productivity. Natural diversity in the catalytic properties of Rubisco indicates possibilities for improvement. Oceanic phytoplankton contain some of the most efficient Rubisco enzymes, and diatoms in particular are responsible for a significant proportion of total marine primary production as well as being a major source of CO2 sequestration in polar cold waters. Until now, the biochemical properties and three-dimensional structures of Rubisco from diatoms were unknown. Here, diatoms from arctic waters were collected, cultivated, and analyzed for their CO2-fixing capability. We characterized the kinetic properties of five and determined the crystal structures of four Rubiscos selected for their high CO2-fixing efficiency. The DNA sequences of the rbcL and rbcS genes of the selected diatoms were similar, reflecting their close phylogenetic relationship. The Vmax and Km for the oxygenase and carboxylase activities at 25 °C and the specificity factors (Sc/o) at 15, 25, and 35 °C were determined. The Sc/o values were high, approaching those of mono- and dicot plants, thus exhibiting good selectivity for CO2 relative to O2 Structurally, diatom Rubiscos belong to form I C/D, containing small subunits characterized by a short βA-βB loop and a C-terminal extension that forms a β-hairpin structure (βE-βF loop). Of note, the diatom Rubiscos featured a number of posttranslational modifications of the large subunit, including 4-hydroxyproline, β-hydroxyleucine, hydroxylated and nitrosylated cysteine, mono- and dihydroxylated lysine, and trimethylated lysine. Our studies suggest adaptation toward achieving efficient CO2 fixation in arctic diatom Rubiscos.

Keywords: CO2/O2 specificity; carbon fixation; crystal structure; diatoms; enzyme kinetics; posttranslational modification (PTM); ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Carbon Dioxide / metabolism*
  • Crystallography, X-Ray
  • Diatoms / enzymology*
  • Hydroxylation
  • Kinetics
  • Nitrosation
  • Phylogeny
  • Protein Conformation
  • Protein Folding
  • Protein Processing, Post-Translational*
  • Ribulose-Bisphosphate Carboxylase / chemistry*
  • Ribulose-Bisphosphate Carboxylase / genetics
  • Ribulose-Bisphosphate Carboxylase / metabolism*
  • Structure-Activity Relationship


  • Carbon Dioxide
  • Ribulose-Bisphosphate Carboxylase

Associated data

  • PDB/5MZ2
  • PDB/5N9Z
  • PDB/6FTL
  • PDB/5OYA
  • PDB/1BWV