4PA8 | pdb_00004pa8

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

• PDB DOI: https://doi.org/10.2210/pdb4PA8/pdb

• Classification: HYDROLASE
• Organism(s): Saccharolobus solfataricus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-04-07 Released: 2015-04-01 
• Deposition Author(s): Beck, T., Garrabou Pi, X., Hilvert, D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.177 (Depositor), 0.169 (DCC) 
• R-Value Work: 
  0.139 (Depositor), 0.136 (DCC) 

Starting Model: experimental

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

• PubMed: 25777153 
• DOI: https://doi.org/10.1002/anie.201500217
• Primary Citation 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, RA95.5-8, 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).

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 30.52 kDa 
• Atom Count: 2,251 
• Modeled Residue Count: 236 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
retro-aldolase	A	258	Saccharolobus solfataricus	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2K6	B [auth A]	(3R)-3-(4-methoxyphenyl)-5-oxohexanenitrile C13 H15 N O2 UZVHUQSCXULJKG-GFCCVEGCSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.177 (Depositor), 0.169 (DCC) 
• R-Value Work:  0.139 (Depositor), 0.136 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.557	α = 90
b = 68.804	β = 90
c = 69.341	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
SHELXL	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-01 
Deposition Author(s): Beck, T., Garrabou Pi, X., Hilvert, D.

Revision History  

• Version 1.0: 2015-04-01
  Type: Initial release
  
• Version 1.1: 2015-05-13
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Refinement description
• Version 2.0: 2025-10-01
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary