9H87 | pdb_00009h87

Crystal structure of LmrR variant V15aY with Val15 replaced by 3-aminotyrosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.268 (Depositor), 0.279 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Genetically encoded 3-aminotyrosine as catalytic residue in a designer Friedel-Crafts alkylase.

Brouwer, B.Della-Felice, F.Thunnissen, A.W.H.Roelfes, G.

(2025) Chem Sci 16: 8721-8728

  • DOI: https://doi.org/10.1039/d5sc01055a
  • Primary Citation of Related Structures:  
    9H87, 9H88

  • PubMed Abstract: 

    Genetic incorporation of noncanonical amino acids (ncAAs) harbouring catalytic side chains into proteins allows the creation of enzymes able to catalyse reactions that have no equivalent in nature. Here, we present for the first time the use of the ncAA 3-aminotyrosine (aY) as catalytic residue in a designer enzyme for iminium activation catalysis. Incorporation of aY into protein scaffold LmrR gave rise to an artificial Friedel-Crafts (FC) alkylase exhibiting complementary enantioselectivity to a previous FC-alkylase design using p -aminophenylalanine as catalytic residue in the same protein. The new FC-alkylase was optimized by directed evolution to afford a quadruple mutant that showed increased activity and excellent enantioselectivity (up to 95% ee). X-ray crystal structures of the parent and evolved designer enzymes suggest that the introduced mutations cause a narrowing of the active site and a reorientation of the catalytic -NH 2 group. Furthermore, the evolved FC-alkylase was applied in whole-cell catalysis, facilitated by the straightforward incorporation of aY. Our work demonstrates that aY is a valuable addition to the biochemists toolbox for creating artificial enzymes.


  • Organizational Affiliation
    • Stratingh Institute for Chemistry, University of Groningen Nijenborgh 3 9747 AG Groningen The Netherlands j.g.roelfes@rug.nl.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulator, PadR-like family131Lactococcus cremoris subsp. cremoris MG1363Mutation(s): 3 
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
TY2
Query on TY2
A
L-PEPTIDE LINKINGC9 H12 N2 O3TYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.268 (Depositor), 0.279 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: P 32 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.714α = 90
b = 70.714β = 90
c = 59.838γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union885396
Netherlands Organisation for Scientific Research (NWO)NetherlandsOCENW.KLEIN.143

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-30
    Type: Initial release
  • Version 1.1: 2025-05-07
    Changes: Database references
  • Version 1.2: 2025-06-04
    Changes: Database references