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: 1.2 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.139 

wwPDB Validation 3D Report Full Report


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

  • 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 promiscuit ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
retro-aldolase
A
258N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
2K6
Query on 2K6

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Download CCD File 
A
(3R)-3-(4-methoxyphenyl)-5-oxohexanenitrile
C13 H15 N O2
UZVHUQSCXULJKG-GFCCVEGCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 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 = 90.00
b = 68.804β = 90.00
c = 69.341γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
SHELXLrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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