7B1W

Crystal structure of plastidial ribulose epimerase RPE1 from the model alga Chlamydomonas reinhardtii

Summary for 7B1W

• Entry DOI: 10.2210/pdb7b1w/pdb
• Descriptor: Ribulose-phosphate 3-epimerase, ZINC ION (3 entities in total)
• Functional Keywords: calvin-benson cycle, photosynthesis, ribulose, ribose, epimerase, chloroplast, carbon fixation, isomerase
• Biological source: Chlamydomonas reinhardtii
• Total number of polymer chains: 12
• Total formula weight: 322517.30

Authors

Henri, J.,Zaffagnini, M.,Tedesco, D.,Crozet, P.,Lemaire, S.D. (deposition date: 2020-11-25, release date: 2021-12-08, Last modification date: 2024-05-01)

Primary citation

Meloni, M.,Fanti, S.,Tedesco, D.,Gurrieri, L.,Trost, P.,Fermani, S.,Lemaire, S.D.,Zaffagnini, M.,Henri, J.
Characterization of chloroplast ribulose-5-phosphate-3-epimerase from the microalga Chlamydomonas reinhardtii.
Plant Physiol., 2023

PubMed Abstract: Carbon fixation relies on Rubisco and 10 additional enzymes in the Calvin-Benson-Bassham cycle. Epimerization of xylulose-5-phosphate (Xu5P) into ribulose-5-phosphate (Ru5P) contributes to the regeneration of ribulose-1,5-bisphosphate, the substrate of Rubisco. Ribulose-5-phosphate-3-epimerase (RPE, EC 5.1.3.1) catalyzes the formation of Ru5P, but it can also operate in the pentose-phosphate pathway by catalyzing the reverse reaction. Here, we describe the structural and biochemical properties of the recombinant RPE isoform 1 from Chlamydomonas (Chlamydomonas reinhardtii) (CrRPE1). The enzyme is a homo-hexamer that contains a zinc ion in the active site and exposes a catalytic pocket on the top of an α8β8 triose isomerase-type barrel as observed in structurally solved RPE isoforms from both plant and non-plant sources. By optimizing and developing enzyme assays to monitor the reversible epimerization of Ru5P to Xu5P and vice versa, we determined the catalytic parameters that differ from those of other plant paralogs. Despite being identified as a putative target of multiple thiol-based redox modifications, CrRPE1 activity is not affected by both reductive and oxidative treatments, indicating that enzyme catalysis is insensitive to possible redox alterations of cysteine residues. We mapped phosphorylation sites on the crystal structure, and the specific location at the entrance of the catalytic cleft supports a phosphorylation-based regulatory mechanism. This work provides an accurate description of the structural features of CrRPE1 and an in-depth examination of its catalytic and regulatory properties highlighting the physiological relevance of this enzyme in the context of photosynthetic carbon fixation.

PubMed: 38134324
DOI: 10.1093/plphys/kiad680

Experimental method

X-RAY DIFFRACTION (1.935 Å)