6A5F image
Entry Detail
PDB ID:
6A5F
Title:
The structure of [4+2] and [6+4] cyclase in the biosynthetic pathway of nargenicin
Biological Source:
PDB Version:
Deposition Date:
2018-06-23
Release Date:
2019-02-06
Method Details:
Experimental Method:
Resolution:
2.05 Å
R-Value Free:
0.18
R-Value Work:
0.15
R-Value Observed:
0.16
Space Group:
P 32 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:NgnD
Chain IDs:A, B
Chain Length:165
Number of Molecules:2
Biological Source:Nocardia argentinensis ATCC 31306
Primary Citation
Enzyme-catalysed [6+4] cycloadditions in the biosynthesis of natural products.
Nature 568 122 126 (2019)
PMID: 30867595 DOI: 10.1038/s41586-019-1021-x

Abstact

Pericyclic reactions are powerful transformations for the construction of carbon-carbon and carbon-heteroatom bonds in organic synthesis. Their role in biosynthesis is increasingly apparent, and mechanisms by which pericyclases can catalyse reactions are of major interest1. [4+2] cycloadditions (Diels-Alder reactions) have been widely used in organic synthesis2 for the formation of six-membered rings and are now well-established in biosynthesis3-6. [6+4] and other 'higher-order' cycloadditions were predicted7 in 1965, and are now increasingly common in the laboratory despite challenges arising from the generation of a highly strained ten-membered ring system8,9. However, although enzyme-catalysed [6+4] cycloadditions have been proposed10-12, they have not been proven to occur. Here we demonstrate a group of enzymes that catalyse a pericyclic [6+4] cycloaddition, which is a crucial step in the biosynthesis of streptoseomycin-type natural products. This type of pericyclase catalyses [6+4] and [4+2] cycloadditions through a single ambimodal transition state, which is consistent with previous proposals11,12. The [6+4] product is transformed to a less stable [4+2] adduct via a facile Cope rearrangement, and the [4+2] adduct is converted into the natural product enzymatically. Crystal structures of three pericyclases, computational simulations of potential energies and molecular dynamics, and site-directed mutagenesis establish the mechanism of this transformation. This work shows how enzymes are able to catalyse concerted pericyclic reactions involving ambimodal transition states.

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