9AUB

PLP-dependent BesB-F231Y variant holoenzyme

Summary for 9AUB

• Entry DOI: 10.2210/pdb9aub/pdb
• Related: 9AUA
• Descriptor: BesB F231Y variant, 1,2-ETHANEDIOL, GLYCEROL, ... (5 entities in total)
• Functional Keywords: pyridoxal 5'-phosphate, alkyne, biosynthetic protein
• Biological source: Streptomyces achromogenes subsp. achromogenes
• Total number of polymer chains: 1
• Total formula weight: 58021.69

Authors

Hedges, J.B.,Ryan, K.S. (deposition date: 2024-02-28, release date: 2025-07-02, Last modification date: 2025-07-09)

Primary citation

Hedges, J.B.,Marchand, J.A.,Calvo-Tusell, C.,Wei, Z.W.,Millar, D.C.,Garcia-Borras, M.,Chang, M.C.Y.,Ryan, K.S.
Terminal alkyne formation by a pyridoxal phosphate-dependent enzyme.
Nat.Chem.Biol., 2025

PubMed Abstract: Terminal alkyne-containing natural products can undergo the bio-orthogonal 'click' reaction of Cu(I)-catalyzed azide-alkyne cycloaddition. Recently, an enzymatic mechanism for terminal alkyne formation was discovered in the biosynthesis of L-β-ethynylserine where the pyridoxal phosphate-dependent enzyme BesB forms a rare terminal alkyne-containing amino acid, L-propargylglycine, from a vinyl halide precursor, 4-chloro-L-allylglycine. Here we present the 1.3-Å-resolution crystal structure of BesB with detailed mechanistic and computational studies. We demonstrate that BesB can reversibly catalyze the exchange of the halogen in various 4-halo-allyl-L-glycines, implying the existence of an allene intermediate, which we then also observe. Taken together, this work supports a mechanism whereby an allene is formed from deprotonation-driven halogen loss and the terminal alkyne is then formed by isomerization of the allene. Our work further expands our understanding of the catalytic repertoire of pyridoxal phosphate-dependent enzymes and will enable development of metal-free allene-forming and alkyne-forming biocatalysts.

PubMed: 40562852
DOI: 10.1038/s41589-025-01954-9

Experimental method

X-RAY DIFFRACTION (1.49 Å)