6H7H

Crystal structure of redox-sensitive phosphoribulokinase (PRK) from Arabidopsis thaliana

Summary for 6H7H

• Entry DOI: 10.2210/pdb6h7h/pdb
• Descriptor: Phosphoribulokinase, chloroplastic (2 entities in total)
• Functional Keywords: transferase, kinase, atp binding, photosynthesis
• Biological source: Arabidopsis thaliana (thale cress)
• Total number of polymer chains: 2
• Total formula weight: 79023.74

Authors

Fermani, S.,Sparla, F.,Gurrieri, L.,Falini, G.,Trost, P. (deposition date: 2018-07-31, release date: 2019-04-10, Last modification date: 2024-01-17)

Primary citation

Gurrieri, L.,Del Giudice, A.,Demitri, N.,Falini, G.,Pavel, N.V.,Zaffagnini, M.,Polentarutti, M.,Crozet, P.,Marchand, C.H.,Henri, J.,Trost, P.,Lemaire, S.D.,Sparla, F.,Fermani, S.
ArabidopsisandChlamydomonasphosphoribulokinase crystal structures complete the redox structural proteome of the Calvin-Benson cycle.
Proc.Natl.Acad.Sci.USA, 116:8048-8053, 2019

PubMed Abstract: In land plants and algae, the Calvin-Benson (CB) cycle takes place in the chloroplast, a specialized organelle in which photosynthesis occurs. Thioredoxins (TRXs) are small ubiquitous proteins, known to harmonize the two stages of photosynthesis through a thiol-based mechanism. Among the 11 enzymes of the CB cycle, the TRX target phosphoribulokinase (PRK) has yet to be characterized at the atomic scale. To accomplish this goal, we determined the crystal structures of PRK from two model species: the green alga (PRK) and the land plant (PRK). PRK is an elongated homodimer characterized by a large central β-sheet of 18 strands, extending between two catalytic sites positioned at its edges. The electrostatic surface potential of the catalytic cavity has both a positive region suitable for binding the phosphate groups of substrates and an exposed negative region to attract positively charged TRX-f. In the catalytic cavity, the regulatory cysteines are 13 Å apart and connected by a flexible region exclusive to photosynthetic eukaryotes-the clamp loop-which is believed to be essential for oxidation-induced structural rearrangements. Structural comparisons with prokaryotic and evolutionarily older PRKs revealed that both PRK and PRK have a strongly reduced dimer interface and an increased number of random-coiled regions, suggesting that a general loss in structural rigidity correlates with gains in TRX sensitivity during the molecular evolution of PRKs in eukaryotes.

PubMed: 30923119
DOI: 10.1073/pnas.1820639116

Experimental method

X-RAY DIFFRACTION (2.471 Å)