9FD9 image
Entry Detail
PDB ID:
9FD9
Keywords:
Title:
Re-engineered peroxygenase variant of 2-deoxy-D-ribose-5-phosphate aldolase, Schiff-base complex with 4-nitro-cinnamaldehyde
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2024-05-16
Release Date:
2025-03-12
Method Details:
Experimental Method:
Resolution:
1.52 Å
R-Value Free:
0.21
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Deoxyribose-phosphate aldolase
Mutations:T18S, L20S, D22G, D24Y, C47S, I48V, F52S, K172R, T197S, P202V, A203T, R207S, G236S, S239G
Chain IDs:A, B
Chain Length:267
Number of Molecules:2
Biological Source:Escherichia coli
Primary Citation
Engineering 2-Deoxy-D-ribose-5-phosphate Aldolase for anti- and syn-Selective Epoxidations of alpha , beta-Unsaturated Aldehydes.
Angew.Chem.Int.Ed.Engl. 64 e202503054 e202503054 (2025)
PMID: 39993220 DOI: 10.1002/anie.202503054

Abstact

The enzyme 2-deoxy-D-ribose-5-phosphate aldolase (DERA) naturally catalyzes the reversible aldol addition between acetaldehyde and D-glyceraldehyde-3-phosphate to yield 2-deoxy-D-ribose-5-phosphate. Herein we describe the redesign of DERA into a proficient non-natural peroxygenase that promotes the asymmetric epoxidation of various α,β-unsaturated aldehydes. This repurposed aldolase, named DERA-EP, is able to utilize H2O2 to accomplish both anti- and syn-selective epoxidations of various α,β-unsaturated aldehydes to give the corresponding epoxides with moderate to high diastereoselectivity (diastereomeric ratio up to 99 : 1) and excellent enantioselectivity (enantiomeric ratio up to 99 : 1). Crystallographic analysis of DERA-EP in a substrate-free and substrate-bound state provides a structural context for the evolved activity, a clear explanation for the high enantioselectivity, and compelling evidence for catalysis via enzyme-bound iminium ion intermediates. The unprecedented anti-selectivity of DERA-EP with multiple α,β-unsaturated aldehydes is complementary to the syn-selectivity of previously reported enzyme-, metal- and organo-catalysts, making DERA-EP an attractive new asset to the toolbox of epoxidation catalysts.

Legend

Protein

Chemical

Disease

Primary Citation of related structures