8HWY | pdb_00008hwy

Ancestral imine reductase mutant N559_M6

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

  • Deposited: 2023-01-03 Released: 2024-01-10 
  • Deposition Author(s): Zhu, X.X.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 
    0.225 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Model: in silico
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Literature

Evolutionary insights into the stereoselectivity of imine reductases based on ancestral sequence reconstruction.

Zhu, X.X.Zheng, W.Q.Xia, Z.W.Chen, X.R.Jin, T.Ding, X.W.Chen, F.F.Chen, Q.Xu, J.H.Kong, X.D.Zheng, G.W.

(2024) Nat Commun 15: 10330-10330

  • DOI: https://doi.org/10.1038/s41467-024-54613-3
  • Primary Citation of Related Structures:  
    8HWY, 8JKU

  • PubMed Abstract: 

    The stereoselectivity of enzymes plays a central role in asymmetric biocatalytic reactions, but there remains a dearth of evolution-driven biochemistry studies investigating the evolutionary trajectory of this vital property. Imine reductases (IREDs) are one such enzyme that possesses excellent stereoselectivity, and stereocomplementary members are pervasive in the family. However, the regulatory mechanism behind stereocomplementarity remains cryptic. Herein, we reconstruct a panel of active ancestral IREDs and trace the evolution of stereoselectivity from ancestors to extant IREDs. Combined with coevolution analysis, we reveal six historical mutations capable of recapitulating stereoselectivity evolution. An investigation of the mechanism with X-ray crystallography shows that they collectively reshape the substrate-binding pocket to regulate stereoselectivity inversion. In addition, we construct an empirical fitness landscape and discover that epistasis is prevalent in stereoselectivity evolution. Our findings emphasize the power of ASR in circumventing the time-consuming large-scale mutagenesis library screening for identifying mutations that change functions and support a Darwinian premise from a molecular perspective that the evolution of biological functions is a stepwise process.


  • Organizational Affiliation
    • State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ancestral imine reductase mutant N559_M6
A, B
297EscherichiaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free:  0.225 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.336α = 90
b = 71.762β = 113.2
c = 65.108γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHENIXphasing
DIALSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2024-01-10 
  • Deposition Author(s): Zhu, X.X.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21878085

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-10
    Type: Initial release
  • Version 1.1: 2024-12-11
    Changes: Database references, Structure summary