9FD9 | pdb_00009fd9

Re-engineered peroxygenase variant of 2-deoxy-D-ribose-5-phosphate aldolase, Schiff-base complex with 4-nitro-cinnamaldehyde


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 
    0.218 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Engineering 2-Deoxy-D-ribose-5-phosphate Aldolase for anti- and syn-Selective Epoxidations of alpha , beta-Unsaturated Aldehydes.

Zhou, H.Kunzendorf, A.Xu, G.Frietema, H.O.T.Thunnissen, A.W.H.Poelarends, G.J.

(2025) Angew Chem Int Ed Engl 64: e202503054-e202503054

  • DOI: https://doi.org/10.1002/anie.202503054
  • Primary Citation Related Structures: 
    9FD7, 9FD8, 9FD9

  • PubMed Abstract: 

    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 H 2 O 2 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.


  • Organizational Affiliation
    • Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The, Netherlands.

Macromolecule Content 

  • Total Structure Weight: 57.88 kDa 
  • Atom Count: 3,990 
  • Modeled Residue Count: 486 
  • Deposited Residue Count: 534 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Deoxyribose-phosphate aldolase
A, B
267Escherichia coliMutation(s): 13 
Gene Names: deoCEcolC_3675
EC: 4.1.2.4
UniProt
Find proteins for P0A6L0 (Escherichia coli (strain K12))
Explore P0A6L0 
Go to UniProtKB:  P0A6L0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6L0
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free:  0.218 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.095α = 90
b = 72.531β = 96.27
c = 70.688γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands Organisation for Scientific Research (NWO)Netherlands724.016.002

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release
  • Version 1.1: 2025-05-21
    Changes: Database references
  • Version 1.2: 2026-04-15
    Changes: Data collection, Database references, Derived calculations, Structure summary