4PA8

Crystal structure of a de novo retro-aldolase catalyzing asymmetric Michael additions, with a covalently bound product analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.139 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A Promiscuous De Novo Retro-Aldolase Catalyzes Asymmetric Michael Additions via Schiff Base Intermediates.

Garrabou, X.Beck, T.Hilvert, D.

(2015) Angew Chem Int Ed Engl 54: 5609-5612

  • DOI: 10.1002/anie.201500217
  • Primary Citation of Related Structures:  
    4PA8

  • PubMed Abstract: 
  • Recent advances in computational design have enabled the development of primitive enzymes for a range of mechanistically distinct reactions. Here we show that the rudimentary active sites of these catalysts can give rise to useful chemical promiscuity. Specifically, RA95 ...

    Recent advances in computational design have enabled the development of primitive enzymes for a range of mechanistically distinct reactions. Here we show that the rudimentary active sites of these catalysts can give rise to useful chemical promiscuity. Specifically, RA95.5-8, designed and evolved as a retro-aldolase, also promotes asymmetric Michael additions of carbanions to unsaturated ketones with high rates and selectivities. The reactions proceed by amine catalysis, as indicated by mutagenesis and X-ray data. The inherent flexibility and tunability of this catalyst should make it a versatile platform for further optimization and/or mechanistic diversification by directed evolution.


    Organizational Affiliation

    Laboratory of Organic Chemistry, ETH Zürich, 8093 Zürich (Switzerland); Instituto de Química Avanzada de Cataluña-CSIC, Jordi Girona 18-26, 08034 Barcelona (Spain).



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
retro-aldolaseA258Saccharolobus solfataricusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2K6 (Subject of Investigation/LOI)
Query on 2K6

Download Ideal Coordinates CCD File 
B [auth A](3R)-3-(4-methoxyphenyl)-5-oxohexanenitrile
C13 H15 N O2
UZVHUQSCXULJKG-GFCCVEGCSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A], F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.139 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.557α = 90
b = 68.804β = 90
c = 69.341γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
SHELXLrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-01
    Type: Initial release
  • Version 1.1: 2015-05-13
    Changes: Database references