Re-engineered 2-deoxy-D-ribose-5-phosphate aldolase catalysing asymmetric Michael addition reactions, Schiff base complex with cinnamaldehyde

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.238 

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Unlocking Asymmetric Michael Additions in an Archetypical Class I Aldolase by Directed Evolution.

Kunzendorf, A.Xu, G.van der Velde, J.J.H.Rozeboom, H.J.Thunnissen, A.W.H.Poelarends, G.J.

(2021) ACS Catal 11: 13236-13243

  • DOI: https://doi.org/10.1021/acscatal.1c03911
  • Primary Citation of Related Structures:  
    7P75, 7P76

  • PubMed Abstract: 

    Class I aldolases catalyze asymmetric aldol addition reactions and have found extensive application in the biocatalytic synthesis of chiral β-hydroxy-carbonyl compounds. However, the usefulness of these powerful enzymes for application in other C-C bond-forming reactions remains thus far unexplored. The redesign of class I aldolases to expand their catalytic repertoire to include non-native carboligation reactions therefore continues to be a major challenge. Here, we report the successful redesign of 2-deoxy-d-ribose-5-phosphate aldolase (DERA) from Escherichia coli , an archetypical class I aldolase, to proficiently catalyze enantioselective Michael additions of nitromethane to α,β-unsaturated aldehydes to yield various pharmaceutically relevant chiral synthons. After 11 rounds of directed evolution, the redesigned DERA enzyme (DERA-MA) carried 12 amino-acid substitutions and had an impressive 190-fold enhancement in catalytic activity compared to the wildtype enzyme. The high catalytic efficiency of DERA-MA for this abiological reaction makes it a proficient "Michaelase" with potential for biocatalytic application. Crystallographic analysis provides a structural context for the evolved activity. Whereas an aldolase acts naturally by activating the enzyme-bound substrate as a nucleophile (enamine-based mechanism), DERA-MA instead acts by activating the enzyme-bound substrate as an electrophile (iminium-based mechanism). This work demonstrates the power of directed evolution to expand the reaction scope of natural aldolases to include asymmetric Michael addition reactions and presents opportunities to explore iminium catalysis with DERA-derived catalysts inspired by developments in the organocatalysis field.

  • Organizational Affiliation

    Molecular Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Deoxyribose-phosphate aldolase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
267Escherichia coli 909945-2Mutation(s): 12 
Gene Names: deoCHMPREF1620_02713
Find proteins for V0AAC4 (Escherichia coli 909945-2)
Explore V0AAC4 
Go to UniProtKB:  V0AAC4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV0AAC4
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9Y6 (Subject of Investigation/LOI)
Query on 9Y6

Download Ideal Coordinates CCD File 
M [auth A]
N [auth B]
O [auth C]
P [auth D]
Q [auth E]
M [auth A],
N [auth B],
O [auth C],
P [auth D],
Q [auth E],
R [auth F],
S [auth G],
T [auth H],
U [auth I],
W [auth J],
X [auth K],
Y [auth L]
C9 H8 O
Query on GOL

Download Ideal Coordinates CCD File 
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.238 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.27α = 88.96
b = 92.788β = 88.83
c = 106.894γ = 89.08
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
Cootmodel building
PDB_EXTRACTdata extraction

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: 2021-10-27
    Type: Initial release
  • Version 1.1: 2021-11-24
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description