7Q53

Single Particle Cryo-EM structure of photosynthetic A2B2 glyceraldehyde 3-phosphate dehydrogenase from Spinacia oleracia

Summary for 7Q53

• Entry DOI: 10.2210/pdb7q53/pdb
• Related: 2PKQ
• EMDB information: 13824
• Descriptor: Glyceraldehyde-3-phosphate dehydrogenase B, chloroplastic, Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic,Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic,Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic,Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic, NICOTINAMIDE-ADENINE-DINUCLEOTIDE (3 entities in total)
• Functional Keywords: photosynthesis, calvin-benson cycle, redox regulation, glyceraldehyde-3-phosphate dehydrogenase, oxidoreductase
• Biological source: Spinacia oleracea (spinach); More
• Total number of polymer chains: 4
• Total formula weight: 147743.80

Authors

Marotta, R.,Fermani, S.,Sparla, F.,Trost, P.,Del Giudice, A. (deposition date: 2021-11-02, release date: 2022-11-16, Last modification date: 2024-07-17)

Primary citation

Marotta, R.,Del Giudice, A.,Gurrieri, L.,Fanti, S.,Swuec, P.,Galantini, L.,Falini, G.,Trost, P.,Fermani, S.,Sparla, F.
Unravelling the regulation pathway of photosynthetic AB-GAPDH.
Acta Crystallogr D Struct Biol, 78:1399-1411, 2022

PubMed Abstract: Oxygenic phototrophs perform carbon fixation through the Calvin-Benson cycle. Different mechanisms adjust the cycle and the light-harvesting reactions to rapid environmental changes. Photosynthetic glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a key enzyme in the cycle. In land plants, different photosynthetic GAPDHs exist: the most abundant isoform is formed by AB heterotetramers and the least abundant by A homotetramers. Regardless of the subunit composition, GAPDH is the major consumer of photosynthetic NADPH and its activity is strictly regulated. While A-GAPDH is regulated by CP12, AB-GAPDH is autonomously regulated through the C-terminal extension (CTE) of its B subunits. Reversible inhibition of AB-GAPDH occurs via the oxidation of a cysteine pair located in the CTE and the substitution of NADP(H) with NAD(H) in the cofactor-binding site. These combined conditions lead to a change in the oligomerization state and enzyme inhibition. SEC-SAXS and single-particle cryo-EM analysis were applied to reveal the structural basis of this regulatory mechanism. Both approaches revealed that spinach (AB)-GAPDH oligomers with n = 1, 2, 4 and 5 co-exist in a dynamic system. B subunits mediate the contacts between adjacent tetramers in AB and AB oligomers. The CTE of each B subunit penetrates into the active site of a B subunit of the adjacent tetramer, which in turn moves its CTE in the opposite direction, effectively preventing the binding of the substrate 1,3-bisphosphoglycerate in the B subunits. The whole mechanism is made possible, and eventually controlled, by pyridine nucleotides. In fact, NAD(H), by removing NADP(H) from A subunits, allows the entrance of the CTE into the active site of the B subunit, hence stabilizing inhibited oligomers.

PubMed: 36322422
DOI: 10.1107/S2059798322010014

Experimental method

ELECTRON MICROSCOPY (6.3 Å)