9FUO | pdb_00009fuo

Crystal structure of SNAr1.3 (K39A)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 
    0.231 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9FUO

This is version 1.1 of the entry. See complete history

Literature

Engineered enzymes for enantioselective nucleophilic aromatic substitutions.

Lister, T.M.Roberts, G.W.Hossack, E.J.Zhao, F.Burke, A.J.Johannissen, L.O.Hardy, F.J.Millman, A.A.V.Leys, D.Larrosa, I.Green, A.P.

(2025) Nature 639: 375-381

  • DOI: https://doi.org/10.1038/s41586-025-08611-0
  • Primary Citation Related Structures: 
    9FUG, 9FUL, 9FUO

  • PubMed Abstract: 

    Nucleophilic aromatic substitutions (S N Ar) are amongst the most widely used processes in the pharmaceutical and agrochemical industries 1-4 , allowing convergent assembly of complex molecules through C-C and C-X (X = O, N, S) bond formation. S N Ar reactions are typically carried out using forcing conditions, involving polar aprotic solvents, stoichiometric bases and elevated temperatures, which do not allow for control over reaction selectivity. Despite the importance of S N Ar chemistry, there are only a handful of selective catalytic methods reported that rely on small organic hydrogen-bonding or phase-transfer catalysts 5-11 . Here we establish a biocatalytic approach to stereoselective S N Ar chemistry by uncovering promiscuous S N Ar activity in a designed enzyme featuring an activated arginine 12 . This activity was optimized over successive rounds of directed evolution to afford an engineered biocatalyst, S N Ar1.3, that is 160-fold more efficient than the parent and promotes the coupling of electron-deficient arenes with carbon nucleophiles with near-perfect stereocontrol (>99% e.e.). S N Ar1.3 can operate at a rate of 0.15 s -1 , perform >4000 turnovers and can accept a broad range of electrophilic and nucleophilic coupling partners, including those that allow construction of challenging 1,1-diaryl quaternary stereocentres. Biochemical, structural and computational studies provide insights into the catalytic mechanism of S N Ar1.3, including the emergence of a halide binding pocket shaped by key catalytic residues Arg124 and Asp125. This study brings a landmark synthetic reaction into the realm of biocatalysis to provide an efficient and versatile platform for catalytic S N Ar chemistry.


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

Macromolecule Content 

  • Total Structure Weight: 28.06 kDa 
  • Atom Count: 2,192 
  • Modeled Residue Count: 231 
  • Deposited Residue Count: 242 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chain A242synthetic constructMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free:  0.231 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.188α = 90
b = 70.188β = 90
c = 119.281γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
UK Research and Innovation (UKRI)United KingdomBB/W014483/1
Engineering and Physical Sciences Research CouncilUnited KingdomEP/023755/1

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release
  • Version 1.1: 2025-03-26
    Changes: Database references