7E37

Crystal structure of deoxypodophyllotoxin synthase from Sinopodophyllum hexandrum in complex with 2-oxoglutarate

Summary for 7E37

• Entry DOI: 10.2210/pdb7e37/pdb
• Descriptor: Deoxypodophyllotoxin synthase, FE (III) ION, 2-OXOGLUTARIC ACID, ... (4 entities in total)
• Functional Keywords: non-heme iron/2-oxoglutarate enzyme beta-helix fold deoxypodophyllotoxin biosynthesis carbon-carbon bond formation, biosynthetic protein
• Biological source: Sinopodophyllum hexandrum (Himalayan may apple)
• Total number of polymer chains: 2
• Total formula weight: 72684.10

Authors

Wu, M.-H.,Lin, H.-Y.,Chang, W.-c.,Chien, T.-C.,Chan, N.-L. (deposition date: 2021-02-08, release date: 2021-12-15, Last modification date: 2024-12-11)

Primary citation

Tang, H.,Wu, M.H.,Lin, H.Y.,Han, M.R.,Tu, Y.H.,Yang, Z.J.,Chien, T.C.,Chan, N.L.,Chang, W.C.
Mechanistic analysis of carbon-carbon bond formation by deoxypodophyllotoxin synthase.
Proc.Natl.Acad.Sci.USA, 119:-, 2022

PubMed Abstract: 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.

PubMed: 34969844
DOI: 10.1073/pnas.2113770119

Experimental method

X-RAY DIFFRACTION (2.09 Å)