9G52 | pdb_00009g52

Crystal structure of LmrR with V15 replaced by unnatural amino acid 4-mercaptophenylalanine, Au(I) bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.294 (Depositor), 0.298 (DCC) 
  • R-Value Work: 
    0.245 (Depositor), 0.255 (DCC) 
  • R-Value Observed: 
    0.248 (Depositor) 

Starting Model: experimental
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Literature

Artificial Gold Enzymes Using a Genetically Encoded Thiophenol-Based Noble-Metal-Binding Ligand.

Veen, M.J.Aalbers, F.S.Rozeboom, H.J.Thunnissen, A.W.H.Sauer, D.F.Roelfes, G.

(2025) Angew Chem Int Ed Engl 64: e202421912-e202421912

  • DOI: https://doi.org/10.1002/anie.202421912
  • Primary Citation of Related Structures:  
    9G51, 9G52

  • PubMed Abstract: 

    Incorporating noble metals in artificial metalloenzymes (ArMs) is challenging due to the lack of suitable soft coordinating ligands among natural amino acids. We present a new class of ArMs featuring a genetically encoded noble-metal-binding site based on a non-canonical thiophenol-based amino acid, 4-mercaptophenylalanine (pSHF), incorporated in the transcriptional regulator LmrR through stop codon suppression. We demonstrate that pSHF is an excellent ligand for noble metals in their low oxidation states. The corresponding gold(I) enzyme was characterised by mass spectrometry, UV/Vis spectroscopy and X-ray crystallography and successfully catalysed hydroamination reactions of 2-ethynyl anilines with turnover numbers over 50. Interestingly, two equivalents of gold(I) per protein dimer proved to be required for activity. Up to 98 % regioselectivity in the hydroamination of an ethynylphenylurea substrate was observed, yielding the corresponding phenyl-dihydroquinazolinone product, consistent with a π-activation mechanism by single gold centres. The ArM was optimized by site saturation mutagenesis using an on-bead screening protocol. This resulted in a single mutant that showed higher activity for one class of substrates. This work brings the power of noble-metal catalysis into the realm of enzyme engineering and establishes thiophenols as alternative ligands for noble metals, providing new opportunities in coordination chemistry and catalysis.


  • Organizational Affiliation
    • Stratingh Institute for Chemistry, University of Groningen, 9747 AG, Groningen, the, Netherlands.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulator, PadR-like family
A, B
126Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 0 
Gene Names: llmg_0323
UniProt
Find proteins for A2RI36 (Lactococcus lactis subsp. cremoris (strain MG1363))
Explore A2RI36 
Go to UniProtKB:  A2RI36
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2RI36
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
A1IID
Query on A1IID
A, B
L-PEPTIDE LINKINGC9 H11 N O2 SALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.294 (Depositor), 0.298 (DCC) 
  • R-Value Work:  0.245 (Depositor), 0.255 (DCC) 
  • R-Value Observed: 0.248 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.44α = 90
b = 52.715β = 90
c = 146.194γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union885396

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-25
    Type: Initial release
  • Version 1.1: 2025-03-26
    Changes: Database references