7ZP7

Crystal structure of evolved photoenzyme EnT1.3 (truncated) with bound product

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

  • Deposited: 2022-04-26 Released: 2022-09-28 
  • Deposition Author(s): Hardy, F.J., Levy, C.
  • Funding Organization(s): European Research Council (ERC), Biotechnology and Biological Sciences Research Council (BBSRC), Engineering and Physical Sciences Research Council

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

A designed photoenzyme for enantioselective [2+2] cycloadditions.

Trimble, J.S.Crawshaw, R.Hardy, F.J.Levy, C.W.Brown, M.J.B.Fuerst, D.E.Heyes, D.J.Obexer, R.Green, A.P.

(2022) Nature 611: 709-714

  • DOI: https://doi.org/10.1038/s41586-022-05335-3
  • Primary Citation of Related Structures:  
    7ZP5, 7ZP6, 7ZP7

  • PubMed Abstract: 

    The ability to program new modes of catalysis into proteins would allow the development of enzyme families with functions beyond those found in nature. To this end, genetic code expansion methodology holds particular promise, as it allows the site-selective introduction of new functional elements into proteins as noncanonical amino acid side chains 1-4 . Here we exploit an expanded genetic code to develop a photoenzyme that operates by means of triplet energy transfer (EnT) catalysis, a versatile mode of reactivity in organic synthesis that is not accessible to biocatalysis at present 5-12 . Installation of a genetically encoded photosensitizer into the beta-propeller scaffold of DA_20_00 (ref.  13 ) converts a de novo Diels-Alderase into a photoenzyme for [2+2] cycloadditions (EnT1.0). Subsequent development and implementation of a platform for photoenzyme evolution afforded an efficient and enantioselective enzyme (EnT1.3, up to 99% enantiomeric excess (e.e.)) that can promote intramolecular and bimolecular cycloadditions, including transformations that have proved challenging to achieve selectively with small-molecule catalysts. EnT1.3 performs >300 turnovers and, in contrast to small-molecule photocatalysts, can operate effectively under aerobic conditions and at ambient temperatures. An X-ray crystal structure of an EnT1.3-product complex shows how multiple functional components work in synergy to promote efficient and selective photocatalysis. This study opens up a wealth of new excited-state chemistry in protein active sites and establishes the framework for developing a new generation of enantioselective photocatalysts.


  • Organizational Affiliation

    Department of Chemistry, The University of Manchester, Manchester, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EnT1.3 C
A, B
330synthetic constructMutation(s): 0 
UniProt
Find proteins for Q7SIG4 (Loligo vulgaris)
Explore Q7SIG4 
Go to UniProtKB:  Q7SIG4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7SIG4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JRP (Subject of Investigation/LOI)
Query on JRP

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(1~{R},10~{R},12~{S})-15-oxa-8-azatetracyclo[8.5.0.0^{1,12}.0^{2,7}]pentadeca-2(7),3,5-trien-9-one
C13 H13 N O2
OZWFNGUWVOXWOF-DVYJOKAKSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PBF
Query on PBF
A, B
L-PEPTIDE LINKINGC16 H15 N O3PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.752α = 90
b = 73.958β = 93.46
c = 74.722γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union757991
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M027023/1
Engineering and Physical Sciences Research CouncilUnited KingdomEP/023755/1

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-28
    Type: Initial release
  • Version 1.1: 2022-10-05
    Changes: Database references
  • Version 1.2: 2022-12-07
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection
  • Version 2.1: 2024-01-31
    Changes: Refinement description