9ZO1 image
Deposition Date 2025-12-15
Release Date 2026-06-03
Last Version Date 2026-06-03
Entry Detail
PDB ID:
9ZO1
Keywords:
Title:
Crystal structure of deoxypodophyllotoxin synthase (DPS) complexed with vanadyl(IV)-oxo, succinate and (-)-hydroxy-yatein
Biological Source:
Source Organism(s):
Expression System(s):
Method Details:
Experimental Method:
Resolution:
2.00 Å
R-Value Free:
0.21
R-Value Work:
0.16
R-Value Observed:
0.16
Space Group:
P 21 21 21
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Deoxypodophyllotoxin synthase
Gene (Uniprot):2-ODD
Chain IDs:A, B
Chain Length:318
Number of Molecules:2
Biological Source:Sinopodophyllum hexandrum
Primary Citation
Biocatalytic Applications and Mechanistic Insights of Deoxypodophyllotoxin Synthase.
J.Am.Chem.Soc. 148 16394 16403 (2026)
PMID: 41946671 DOI: 10.1021/jacs.6c03159

Abstact

The lignan (-)-podophyllotoxin possesses significant antiviral and anticancer activities and thus serves as a precursor to several natural products with therapeutic properties. Biosynthesis of podophyllotoxin involves cyclization of (-)-yatein to yield deoxypodophyllotoxin catalyzed by the iron- and alpha-ketoglutarate-dependent (Fe/alpha-KG) oxidase deoxypodophyllotoxin synthase (DPS), which completes the tetracyclic core of podophyllotoxin. Herein, (+)-hydroxy-yatein is also shown to be a substrate for DPS, directly affording (-)-podophyllotoxin as the enzymatic product. Moreover, derivatives of (+)-hydroxy-yatein are also found to be substrates providing synthetic precursors to medicines such as etoposide. Mechanistic analyses utilizing isotopologs and diastereomers of the m-dimethoxy analogue of (+)-hydroxy-yatein indicate antarafacial C-C bond formation during the cyclization reaction and remain consistent with cation-mediated cyclization. A crystallographic study of DPS bound with vanadium(IV) oxide, succinate, and (-)-hydroxy-yatein suggests a subtle interplay of steric interactions between the substrate and the active site that can alter the course of the DPS-catalyzed reaction and thus cyclization versus hydroxylation. Finally, an efficient chemoenzymatic approach to (-)-podophyllotoxin is described that relies only on freeze-dried whole cells after DPS overexpression.

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