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TitleUnravelling the regulation pathway of photosynthetic AB-GAPDH.
Journal, issue, pagesActa Crystallogr D Struct Biol, Vol. 78, Issue Pt 11, Page 1399-1411, Year 2022
Publish dateNov 1, 2022
AuthorsRoberto Marotta / Alessandra Del Giudice / Libero Gurrieri / Silvia Fanti / Paolo Swuec / Luciano Galantini / Giuseppe Falini / Paolo Trost / Simona Fermani / Francesca Sparla /
PubMed AbstractOxygenic phototrophs perform carbon fixation through the Calvin-Benson cycle. Different mechanisms adjust the cycle and the light-harvesting reactions to rapid environmental changes. Photosynthetic ...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.
External linksActa Crystallogr D Struct Biol / PubMed:36322422
MethodsEM (single particle)
Resolution5.7 - 13.0 Å
Structure data

13824

7q53

EMDB-13824, PDB-7q53:
Single Particle Cryo-EM structure of photosynthetic A2B2 glyceraldehyde 3-phosphate dehydrogenase from Spinacia oleracia
Method: EM (single particle) / Resolution: 6.3 Å

13825

7q54

EMDB-13825, PDB-7q54:
Single Particle Cryo-EM structure of photosynthetic A4B4-glyceraldehyde 3-phosphate dehydrogenase from Spinacia oleracia.
Method: EM (single particle) / Resolution: 8.9 Å

13826

7q55

EMDB-13826, PDB-7q55:
Single Particle Cryo-EM structure of photosynthetic A8B8 glyceraldehyde-3-phosphate dehydrogenase hexadecamer (major conformer) from Spinacia oleracia.
Method: EM (single particle) / Resolution: 5.7 Å

13827

7q56

EMDB-13827, PDB-7q56:
Single Particle Cryo-EM structure of photosynthetic A8B8 glyceraldehyde-3-phosphate dehydrogenase (minor conformer) from Spinacia oleracea.
Method: EM (single particle) / Resolution: 7.1 Å

13828

7q57

EMDB-13828, PDB-7q57:
Single Particle Cryo-EM structure of photosynthetic A10B10 glyceraldehyde-3-phospahte dehydrogenase from Spinacia oleracea.
Method: EM (single particle) / Resolution: 13.0 Å

Chemicals

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

Source
  • spinacia oleracea (spinach)
KeywordsOXIDOREDUCTASE / Photosynthesis / Calvin-Benson cycle / redox regulation / glyceraldehyde-3-phosphate dehydrogenase / glyceraldehyde 3-phosphate dehydrogenase

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