9HA0 | pdb_00009ha0

Crystal structure of Cu(II)-bound LmrR_V15Bpy variant BVS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.235 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

An Artificial Copper-Michaelase Featuring a Genetically Encoded Bipyridine Ligand for Asymmetric Additions to Nitroalkenes.

Jiang, R.Casilli, F.Thunnissen, A.W.H.Roelfes, G.

(2025) Angew Chem Int Ed Engl 64: e202423182-e202423182

  • DOI: https://doi.org/10.1002/anie.202423182
  • Primary Citation of Related Structures:  
    9H9W, 9H9X, 9H9Y, 9H9Z, 9HA0

  • PubMed Abstract: 

    Artificial metalloenzymes (ArMs) are an attractive approach to achieving "new to nature" biocatalytic transformations. In this work, a novel copper-dependent artificial Michaelase (Cu_Michaelase) comprising a genetically encoded copper-binding ligand, i. e. (2,2-bipyridin-5-yl)alanine (BpyA), was developed. For the first time, such an ArM containing a non-canonical metal-binding amino acid was successfully optimized through directed evolution. The evolved Cu_Michaelase was applied in the copper-catalyzed asymmetric addition of 2-acetyl azaarenes to nitroalkenes, yielding various γ-nitro butyric acid derivatives, which are precursors for a range of high-value-added pharmaceutically relevant compounds, with good yields and high enantioselectivities (up to >99 % yield and 99 % ee). Additionally, the evolved variant could be further used in a preparative-scale synthesis, providing chiral products for diverse derivatizations. X-ray crystal structure analysis confirmed the binding of Cu(II) ions to the BpyA residues and showed that, in principle, there is sufficient space for the 2-acetyl azaarene substrate to coordinate. Kinetic studies showed that the increased catalytic efficiency of the evolved enzyme is due to improvements in apparent K M for both substrates and a notable threefold increase in apparent k cat for 2-acetyl pyridine. This work illustrates the potential of artificial metalloenzymes exploiting non-canonical metal-binding ligands for new-to-nature biocatalysis.


  • Organizational Affiliation
    • Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 3, 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
131Lactococcus 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.235 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.395α = 90
b = 54.313β = 90
c = 145.734γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



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: 2025-03-05
    Type: Initial release
  • Version 1.1: 2025-05-07
    Changes: Database references