Journal:Acta Cryst F:S2053230X19002693

Crystal structure of phosphoribulokinase from Synechococcus sp. strain PCC 6301

Robert Wilson, Manajit Hayer-Hartl and Andreas Bracher ^[1]

Molecular Tour
Phosphoribulokinase (PRK) catalyses the ATP-dependent phosphorylation of ribulose-5-phosphate to ribulose-1,5-bisphosphate. The enzyme accompanies Rubisco in autotrophic organisms and both are unique to the Calvin-Benson-Bassham (CBB) cycle of photosynthesis. Isoforms of PRK can be grouped in three classes, which occur in proteobacteria, archaea and photosynthetic organisms respectively. The crystal structure of PRK from the cyanobacterium Synechococcus sp. PCC 6301 presents a structural model for PRK from photosynthetic organisms, such as β-cyanobacteria, most green and red eukaryotic algae, and plants. The enzyme is dimeric and has an alpha/beta-fold with an 18-stranded beta-sheet at its core.

Regulation of PRK enzyme activity in response to light controls carbon fixation during photosynthesis. This occurs via reversible formation of disulfide bonds during dark inactivation and complex formation with the adaptor protein CP12 and glyceraldehyde-3-phosphate dehydrogenase, another CBB cycle enzyme. Interestingly, we find a disulphide bond between Cys40 and the P-loop residue Cys18 in our crystal structure, revealing the structural basis for redox-inactivation of PRK activity. A second disulphide bond appears to rigidify the dimer interface and may thereby contribute to regulation by the adaptor protein CP12 and glyceraldehyde-3-phosphate dehydrogenase into a supramolecular complex within which both enzymes are inhibited.

Perpendicular views of the asymmetric unit in the Syn6301-PRK crystal lattice:

• .
• .

The PRK chains A and B are shown as green and yellow ribbons, respectively. The disulphide bonds are represented as yellow sticks. N- and C-termini are indicated.

Comparison of the active sites in Syn6301-PRK, MhPRK and uridine kinase:

. The Cys18-Cys40 disulphide bond is represented by yellow stick. Secondary structure elements are indicated. The red pointer indicates the Walker A motif (P-loop).

(PDB entry 5b3f; (Kono et al., 2017^[2])) in the apo state. The similar view as in the previous scene. The red pointer indicates the Walker A motif (P-loop).

(PDB entry 3W8R; (Tomoike et al., 2013)) in the substrate-bound state. The substrates cytidine (Ctn) and AMP-PCP (ATP) are presented as cyan and magenta sticks, respectively. The helical hairpin acting as a lid above the substrate binding sites is indicated.

References

1. ↑ Wilson RH, Hayer-Hartl M, Bracher A. Crystal structure of phosphoribulokinase from Synechococcus sp. strain PCC 6301. Acta Crystallogr F Struct Biol Commun. 2019 Apr 1;75(Pt 4):278-289. doi:, 10.1107/S2053230X19002693. Epub 2019 Apr 2. PMID:30950829 doi:http://dx.doi.org/10.1107/S2053230X19002693
2. ↑ Kono T, Mehrotra S, Endo C, Kizu N, Matusda M, Kimura H, Mizohata E, Inoue T, Hasunuma T, Yokota A, Matsumura H, Ashida H. A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea. Nat Commun. 2017 Jan 13;8:14007. doi: 10.1038/ncomms14007. PMID:28082747 doi:http://dx.doi.org/10.1038/ncomms14007