7q56 | pdb_00007q56

Single Particle Cryo-EM structure of photosynthetic A8B8 glyceraldehyde-3-phosphate dehydrogenase (minor conformer) from Spinacia oleracea.

spinqualitylabelsall models 7q56, resolution 7.10Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 7q56 is a 16 chain structure with sequence from Spinacia oleracea. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: Electron Microscopy, Resolution 7.1Å Ligands: NAD Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function G3PA_SPIOL Publication Abstract from PubMed 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 A(2)B(2) heterotetramers and the least abundant by A(4) homotetramers. Regardless of the subunit composition, GAPDH is the major consumer of photosynthetic NADPH and its activity is strictly regulated. While A(4)-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 (A(2)B(2))(n)-GAPDH oligomers with n = 1, 2, 4 and 5 co-exist in a dynamic system. B subunits mediate the contacts between adjacent tetramers in A(4)B(4) and A(8)B(8) 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. Unravelling the regulation pathway of photosynthetic AB-GAPDH.,Marotta R, Del Giudice A, Gurrieri L, Fanti S, Swuec P, Galantini L, Falini G, Trost P, Fermani S, Sparla F Acta Crystallogr D Struct Biol. 2022 Nov 1;78(Pt 11):1399-1411. doi: , 10.1107/S2059798322010014. Epub 2022 Oct 27. PMID:36322422 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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