9FYU | pdb_00009fyu

Crystal structure of the engineered photoenzyme VEnT1.0

  • Classification: BIOSYNTHETIC PROTEIN
  • Organism(s): Loligo vulgaris
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2024-07-04 Released: 2025-05-14 
  • Deposition Author(s): Hardy, F.J., Roberts, G.W.
  • Funding Organization(s): Engineering and Physical Sciences Research Council, Biotechnology and Biological Sciences Research Council (BBSRC), European Research Council (ERC)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 
    0.174 (Depositor), 0.178 (DCC) 
  • R-Value Work: 
    0.143 (Depositor), 0.148 (DCC) 
  • R-Value Observed: 
    0.144 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Efficient and selective energy transfer photoenzymes powered by visible light.

Crawshaw, R.Smithson, R.Hofer, J.Hardy, F.J.Roberts, G.W.Trimble, J.S.Kohn, A.R.Levy, C.W.Drost, D.A.Merten, C.Heyes, D.J.Obexer, R.Bach, T.Green, A.P.

(2025) Nat Chem 17: 1083-1090

  • DOI: https://doi.org/10.1038/s41557-025-01820-0
  • Primary Citation of Related Structures:  
    9FYU, 9FYV, 9G65

  • PubMed Abstract: 

    The development of [2 + 2] cyclases containing benzophenone triplet sensitizers highlights the potential of engineered enzymes as a platform for stereocontrolled energy transfer photocatalysis. However, the suboptimal photophysical features of benzophenone necessitates the use of ultraviolet light, limits photochemical efficiency and restricts the range of chemistries accessible. Here we engineer an orthogonal Methanococcus jannaschii tyrosyl-tRNA synthetase/tRNA pair for encoding thioxanthone triplet sensitizers into proteins, which can efficiently harness visible light to drive photochemical conversions. Initially, we developed an enantioselective [2 + 2] cyclase that is orders of magnitude more efficient than our previously developed photoenzymes (k cat  = 13 s -1 , >1,300 turnovers). To demonstrate that thioxanthone-containing enzymes can enable more challenging photochemical conversions, we developed a second oxygen-tolerant enzyme that can steer selective C-H insertions of excited quinolone substrates to afford spirocyclic β-lactams with high selectivity (99% e.e., 22:1 d.r.). This photoenzyme also suppresses a competing substrate decomposition pathway observed with small-molecule sensitizers, underscoring the ability of engineered enzymes to control the fate of excited-state intermediates.


  • Organizational Affiliation
    • Department of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Diisopropyl-fluorophosphatase
A, B
326Loligo vulgarisMutation(s): 0 
EC: 3.8.2.2
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
A1IHG
Query on A1IHG
A, B
L-PEPTIDE LINKINGC16 H13 N O3 SPHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free:  0.174 (Depositor), 0.178 (DCC) 
  • R-Value Work:  0.143 (Depositor), 0.148 (DCC) 
  • R-Value Observed: 0.144 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.729α = 90
b = 73.437β = 94.163
c = 74.121γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Engineering and Physical Sciences Research CouncilUnited KingdomEP/W524347/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/W014483/1
European Research Council (ERC)European Union833337

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-14
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Database references