6YPI

Structure of the engineered metallo-Diels-Alderase DA7 W16G,K58Q,L77R,T78R


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Efficient Lewis acid catalysis of an abiological reaction in a de novo protein scaffold.

Basler, S.Studer, S.Zou, Y.Mori, T.Ota, Y.Camus, A.Bunzel, H.A.Helgeson, R.C.Houk, K.N.Jimenez-Oses, G.Hilvert, D.

(2021) Nat Chem 13: 231-235

  • DOI: https://doi.org/10.1038/s41557-020-00628-4
  • Primary Citation of Related Structures:  
    6YPI, 7BWW

  • PubMed Abstract: 

    New enzyme catalysts are usually engineered by repurposing the active sites of natural proteins. Here we show that design and directed evolution can be used to transform a non-natural, functionally naive zinc-binding protein into a highly active catalyst for an abiological hetero-Diels-Alder reaction. The artificial metalloenzyme achieves >10 4 turnovers per active site, exerts absolute control over reaction pathway and product stereochemistry, and displays a catalytic proficiency (1/K TS  = 2.9 × 10 10  M -1 ) that exceeds all previously characterized Diels-Alderases. These properties capitalize on effective Lewis acid catalysis, a chemical strategy for accelerating Diels-Alder reactions common in the laboratory but so far unknown in nature. Extension of this approach to other metal ions and other de novo scaffolds may propel the design field in exciting new directions.


  • Organizational Affiliation

    Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DA7 W16G,K58Q,L77R,T78R97synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.237α = 90
b = 35.015β = 109.81
c = 43.229γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
AutoSolphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-28
    Type: Initial release
  • Version 1.1: 2021-11-10
    Changes: Data collection, Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection