Structure of Rubisco from Arabidopsis thaliana in complex with 2-carboxyarabinitol-1,5-bisphosphate

Abstract

The crystal structure of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from Arabidopsis thaliana is reported at 1.5 Å resolution. In light of the importance of A. thaliana as a model organism for understanding higher plant biology, and the pivotal role of Rubisco in photosynthetic carbon assimilation, there has been a notable absence of an A. thaliana Rubisco crystal structure. A. thaliana Rubisco is an L₈S₈ hexadecamer comprising eight plastome-encoded catalytic large (L) subunits and eight nuclear-encoded small (S) subunits. A. thaliana produces four distinct small-subunit isoforms (RbcS1A, RbcS1B, RbcS2B and RbcS3B), and this crystal structure provides a snapshot of A. thaliana Rubisco containing the low-abundance RbcS3B small-subunit isoform. Crystals were obtained in the presence of the transition-state analogue 2-carboxy-D-arabinitol-1,5-bisphosphate. A. thaliana Rubisco shares the overall fold characteristic of higher plant Rubiscos, but exhibits an interesting disparity between sequence and structural relatedness to other Rubisco isoforms. These results provide the structural framework to understand A. thaliana Rubisco and the potential catalytic differences that could be conferred by alternative A. thaliana Rubisco small-subunit isoforms.

Keywords: 2-carboxyarabinitol-1,5-bisphosphate; Arabidopsis thaliana; Rubisco; carbon fixation; isoforms; merohedral twinning; rbcS multigene family; ribulose-1,5-bisphosphate carboxylase/oxygenase.

Figure 1

Three-dimensional crystal structure of A. thaliana Rubisco. (a) The L₂S₂ asymmetric unit of A. thaliana Rubisco. LSus are shown in shades of blue and SSus in green. (b) Top (left) and side (right) views of the overall hexadecameric (L₈S₈) structure of A. thaliana Rubisco. One asymmetric unit is shaded as depicted in (a), with the rest of the assembly shaded grey. (c) Structure of the LSu, with the N-terminal domain, C-terminal domain, loop 6 and C-terminal extension shown in yellow, blue, red and cyan, respectively. One 2-CABP molecule is shown bound at the active site. (d) Structure of the SSu, with residues that vary between different A. thaliana Rubisco SSu isoforms shown as orange sticks and numbered according to the mature peptide sequence. (e) 2-CABP is bound at the active site within well defined density. The Mg²⁺ ion that stabilizes the carbamate formed at the catalytic lysine is shown in pink.

Figure 2

Sequences of the four Rubisco SSu isoforms from A. thaliana. The A. thaliana Rubisco structure presented in this study contains the RbcS1B isoform. Transit peptides were removed before analysis and residues are numbered relative to the mature peptide sequence. Conserved residues are boxed, strictly conserved residues have a red background and well conserved residues are shown in red letters. Gaps are represented by dots. Symbols above blocks of sequences annotate the Rubisco SSu secondary structure from PDB entry 5iu0: α, α-helix; β, β-strand; TT, strict β-turn. The secondary-structure elements were named αA, αB, βA, βB, βC and βD according to convention (Knight et al., 1990 ▸). The sequence alignment was created using GenBank accession numbers BAB09355.1 (RbcS1B), AAO29974.1 (RbcS2B), AAL47390.1 (RbcS3B) and AEE34594.1 (RbcS1A).