9FD8 | pdb_00009fd8

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 
    0.185 (Depositor), 0.198 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
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This is version 1.1 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 of 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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: 1.58 Å
  • R-Value Free:  0.185 (Depositor), 0.198 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.084α = 90
b = 72.47β = 96.2
c = 70.885γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACphasing
REFMACrefinement

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