9DRI image
Deposition Date 2024-09-25
Release Date 2025-10-22
Last Version Date 2026-03-25
Entry Detail
PDB ID:
9DRI
Title:
Crystal structure of SphA in complex with VGQ intermedaite
Biological Source:
Source Organism(s):
Expression System(s):
Method Details:
Experimental Method:
Resolution:
1.85 Å
R-Value Free:
0.22
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 1 21 1
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:8-amino-7-oxononanoate syntha
Gene (Uniprot):KXV57_002439
Chain IDs:A (auth: B), B (auth: C)
Chain Length:487
Number of Molecules:2
Biological Source:Aspergillus fumigatus
Primary Citation
Pyridoxal 5'-Phosphate-Dependent Enzymatic Decarboxylative Annulation.
J. Am. Chem. Soc. 148 9709 9719 (2026)
PMID: 41769737 DOI: 10.1021/jacs.5c20979

Abstact

Pyridoxal 5'-phosphate (PLP)-dependent enzymes are among the most versatile biocatalysts, yet transformations involving the Cgamma-nucleophilic vinylglycine quinonoid (VGQ) intermediate remain exceptionally rare. Understanding the untapped reactivity of VGQ could open new avenues for developing PLP-dependent biocatalysts. Here, we establish a biocatalytic platform that artificially accesses and exploits the reactivity of this high-energy intermediate. By reprogramming SphA, a PLP-dependent enzyme that natively catalyzes decarboxylative Claisen condensation, to generate VGQ in situ through facile decarboxylation of vinylaminomalonate, we enable a decarboxylative [3 + 2] annulation between vinylaminomalonate and electron-deficient alkenes. Crystallographic, computational, and mutagenesis studies reveal the key mechanistic features underlying this abiotic transformation. Our findings demonstrate the latent [3 + 2] annulating potential of VGQ and expand the catalytic repertoire of PLP-dependent enzymes, establishing a new strategy for the enzymatic construction of complex carbocyclic architectures.

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