7E37 image
Deposition Date 2021-02-08
Release Date 2021-12-15
Last Version Date 2024-12-11
Entry Detail
PDB ID:
7E37
Title:
Crystal structure of deoxypodophyllotoxin synthase from Sinopodophyllum hexandrum in complex with 2-oxoglutarate
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.09 Å
R-Value Free:
0.23
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 21 21 2
Macromolecular Entities
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
Mechanistic analysis of carbon-carbon bond formation by deoxypodophyllotoxin synthase.
Proc.Natl.Acad.Sci.USA 119 ? ? (2022)
PMID: 34969844 DOI: 10.1073/pnas.2113770119

Abstact

Deoxypodophyllotoxin contains a core of four fused rings (A to D) with three consecutive chiral centers, the last being created by the attachment of a peripheral trimethoxyphenyl ring (E) to ring C. Previous studies have suggested that the iron(II)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenase, deoxypodophyllotoxin synthase (DPS), catalyzes the oxidative coupling of ring B and ring E to form ring C and complete the tetracyclic core. Despite recent efforts to deploy DPS in the preparation of deoxypodophyllotoxin analogs, the mechanism underlying the regio- and stereoselectivity of this cyclization event has not been elucidated. Herein, we report 1) two structures of DPS in complex with 2OG and (±)-yatein, 2) in vitro analysis of enzymatic reactivity with substrate analogs, and 3) model reactions addressing DPS's catalytic mechanism. The results disfavor a prior proposal of on-pathway benzylic hydroxylation. Rather, the DPS-catalyzed cyclization likely proceeds by hydrogen atom abstraction from C7', oxidation of the benzylic radical to a carbocation, Friedel-Crafts-like ring closure, and rearomatization of ring B by C6 deprotonation. This mechanism adds to the known pathways for transformation of the carbon-centered radical in Fe/2OG enzymes and suggests what types of substrate modification are likely tolerable in DPS-catalyzed production of deoxypodophyllotoxin analogs.

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