7DE2 image
Deposition Date 2020-11-01
Release Date 2021-07-14
Last Version Date 2024-05-29
Entry Detail
PDB ID:
7DE2
Keywords:
Title:
iron and alpha-ketoglutarate-dependent endoperoxidase NvfI
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.90 Å
R-Value Free:
0.19
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:NvfI
Chain IDs:A, B
Chain Length:298
Number of Molecules:2
Biological Source:Aspergillus novofumigatus IBT 16806
Primary Citation
Molecular insights into the endoperoxide formation by Fe(II)/ alpha-KG-dependent oxygenase NvfI.
Nat Commun 12 4417 4417 (2021)
PMID: 34285212 DOI: 10.1038/s41467-021-24685-6

Abstact

Endoperoxide-containing natural products are a group of compounds with structurally unique cyclized peroxide moieties. Although numerous endoperoxide-containing compounds have been isolated, the biosynthesis of the endoperoxides remains unclear. NvfI from Aspergillus novofumigatus IBT 16806 is an endoperoxidase that catalyzes the formation of fumigatonoid A in the biosynthesis of novofumigatonin. Here, we describe our structural and functional analyses of NvfI. The structural elucidation and mutagenesis studies indicate that NvfI does not utilize a tyrosyl radical in the reaction, in contrast to other characterized endoperoxidases. Further, the crystallographic analysis reveals significant conformational changes of two loops upon substrate binding, which suggests a dynamic movement of active site during the catalytic cycle. As a result, NvfI installs three oxygen atoms onto a substrate in a single enzyme turnover. Based on these results, we propose a mechanism for the NvfI-catalyzed, unique endoperoxide formation reaction to produce fumigatonoid A.

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