7BWW | pdb_00007bww

Structure of the engineered metallo-Diels-Alderase DA7 W16S

PDB DOI: https://doi.org/10.2210/pdb7BWW/pdb

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

Deposited: 2020-04-16 Released: 2021-04-21
Deposition Author(s): Basler, S., Mori, T., Hilvert, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.205 (Depositor), 0.206 (DCC)
R-Value Work:
0.188 (Depositor), 0.189 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
View more details

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

PubMed: 33526894 Search on PubMed
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 44.36 kDa
Atom Count: 3,353
Modeled Residue Count: 352
Deposited Residue Count: 388
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
metallo-Diels-Alderase DA7 W16S	A, B, C, D	97	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
BEZ Query on BEZ Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth C] MOL2 format, chain E [auth A] MOL2 format, chain L [auth C] mmCIF format, chain E [auth A] mmCIF format, chain L [auth C]	E [auth A], L [auth C]	BENZOIC ACID C₇ H₆ O₂ WPYMKLBDIGXBTP-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth C] Interactions & Density Focus chain E [auth A] Focus chain L [auth C]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain N [auth D] MOL2 format, chain H [auth B] MOL2 format, chain N [auth D] mmCIF format, chain H [auth B] mmCIF format, chain N [auth D]	H [auth B], N [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain N [auth D] Interactions & Density Focus chain H [auth B] Focus chain N [auth D]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D]	G [auth A], J [auth B], M [auth C], P [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain O [auth D] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain O [auth D] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain O [auth D]	I [auth B], K [auth C], O [auth D]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain K [auth C] Focus chain O [auth D] Interactions & Density Focus chain I [auth B] Focus chain K [auth C] Focus chain O [auth D]