6YPI | pdb_00006ypi

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

• PDB DOI: https://doi.org/10.2210/pdb6YPI/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-04-16 Released: 2021-04-28 
• Deposition Author(s): Basler, S., Mori, T., Hilvert, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.230 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

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

• PubMed: 33526894 
• DOI: https://doi.org/10.1038/s41557-020-00628-4
• Primary Citation 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.

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Organizational Affiliation: 
• Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland.
Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA.
Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA. [e-mail].
Ikerbasque, Basque Foundation for Science, and Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Derio, Spain. [e-mail].
Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland. [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 11.43 kDa 
• Atom Count: 887 
• Modeled Residue Count: 87 
• Deposited Residue Count: 97 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DA7 W16G,K58Q,L77R,T78R	A	97	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DMX	D [auth A]	3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE C12 H19 N O3 S MEJASPJNLSQOAG-UHFFFAOYSA-N
BEZ	E [auth A]	BENZOIC ACID C7 H6 O2 WPYMKLBDIGXBTP-UHFFFAOYSA-N
PEG	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.230 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.237	α = 90
b = 35.015	β = 109.81
c = 43.229	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
AutoSol	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-04-28 
Deposition Author(s): Basler, S., Mori, T., Hilvert, D.

Revision History  

• 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