9R2D | pdb_00009r2d

Crystal structure of allylic transferase enzyme ASB1.3 (K39A)

  • Classification: TRANSFERASE
  • Organism(s): Escherichia coli
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2025-04-29 Released: 2026-07-29 
  • Deposition Author(s): Levy, C.W., Ortmayer, M.
  • Funding Organization(s): European Research Council (ERC), Biotechnology and Biological Sciences Research Council (BBSRC), Human Frontier Science Program (HFSP)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 
    0.220 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Protein-confined imidazolium intermediates enable diverse biocatalytic C-C and C-N bond formations.

Birch-Price, Z.Hutton, A.E.Zhao, F.Ortmayer, M.Stoianova, V.Merten, C.Levy, C.Obexer, R.Green, A.P.

(2026) Nat Catal 9: 882-892

  • DOI: https://doi.org/10.1038/s41929-026-01587-8
  • Primary Citation Related Structures: 
    9R2D

  • PubMed Abstract: 

    Developing enzymatic strategies to selectively construct C-C and C-heteroatom bonds is a major objective in modern biocatalysis. Here we combine genetic code reprogramming and laboratory evolution to establish a family of allylic transferase enzymes that can achieve a remarkable breadth of chemistry, enabling the generation of valuable motifs including γ‑butenolides, chiral amines and all-carbon quaternary centres. Our enzymes operate through the formation of electrophilic imidazolium intermediates that can be generated from reagents equipped with a para -nitrophenol leaving group to facilitate high-throughput evolution. These intermediates can be intercepted with diverse carbon and nitrogen nucleophiles to generate densely functionalized products featuring Cβ or Cγ stereocentres. Interestingly, structural analysis suggests that catalysis proceeds through an unanticipated ternary complex involving para -nitrophenol and the incoming substrate nucleophile. This study adds a family of C-C and C-N bond-forming enzymes to the biocatalytic repertoire and illustrates how artificial enzymes can achieve precise control over challenging chemical conversions.


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

Macromolecule Content 

  • Total Structure Weight: 55.55 kDa 
  • Atom Count: 4,061 
  • Modeled Residue Count: 460 
  • Deposited Residue Count: 484 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Crystal structure of ASB1.3
A, B
242Escherichia coliMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
A1JCN
Query on A1JCN
A, B
L-PEPTIDE LINKINGC14 H20 N3 O3HIS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free:  0.220 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.707α = 90
b = 142.475β = 90
c = 119.311γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
DIALSdata scaling
PHASERphasing

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
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/W014483/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/X000974/1
Human Frontier Science Program (HFSP)FranceRGP0004/2022
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/T008725/1

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-29
    Type: Initial release
  • Version 1.1: 2026-09-02
    Changes: Database references