8XYN

Structure of the engineered retro-aldolase RA95.5-8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

An Artificial Enzyme for Asymmetric Nitrocyclopropanation of alpha , beta-Unsaturated Aldehydes-Design and Evolution.

Yu, M.Z.Yuan, Y.Li, Z.J.Kunthic, T.Wang, H.X.Xu, C.Xiang, Z.

(2024) Angew Chem Int Ed Engl 63: e202401635-e202401635

  • DOI: https://doi.org/10.1002/anie.202401635
  • Primary Citation of Related Structures:  
    8XYN

  • PubMed Abstract: 

    The introduction of an abiological catalytic group into the binding pocket of a protein host allows for the expansion of enzyme chemistries. Here, we report the generation of an artificial enzyme by genetic encoding of a non-canonical amino acid that contains a secondary amine side chain. The non-canonical amino acid and the binding pocket function synergistically to catalyze the asymmetric nitrocyclopropanation of α,β-unsaturated aldehydes by the iminium activation mechanism. The designer enzyme was evolved to an optimal variant that catalyzes the reaction at high conversions with high diastereo- and enantioselectivity. This work demonstrates the application of genetic code expansion in enzyme design and expands the scope of enzyme-catalyzed abiological reactions.


  • Organizational Affiliation

    State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, AI for Science (AI4S) Preferred Program, School of Chemical Biology and Biotechnology Peking University Shenzhen Graduate School, University Town of Shenzhen, Nanshan District, 518055, Shenzhen, P. R. China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
retro-aldolase RA95.5-8
A, B
256synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.638α = 90
b = 73.333β = 112.52
c = 94.338γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Shenzhen science and technology programChina20170330155106581
Key-Area Research and Development Program of Guangdong ProvinceChina2020B0303070002

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-24
    Type: Initial release