7WNN | pdb_00007wnn

Crystal structure of Imine Reductase from Actinoalloteichus hymeniacidonis in complex with NADPH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 
    0.199 (Depositor), 0.198 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Tuning an Imine Reductase for the Asymmetric Synthesis of Azacycloalkylamines by Concise Structure-Guided Engineering.

Zhang, J.Liao, D.Chen, R.Zhu, F.Ma, Y.Gao, L.Qu, G.Cui, C.Sun, Z.Lei, X.Gao, S.S.

(2022) Angew Chem Int Ed Engl 61: e202201908-e202201908

  • DOI: https://doi.org/10.1002/anie.202201908
  • Primary Citation Related Structures: 
    7WNN, 7WNW

  • PubMed Abstract: 

    Although imine reductases (IREDs) are emerging as attractive reductive aminases (RedAms), their substrate scope is still narrow, and rational engineering is rare. Focusing on hydrogen bond reorganization and cavity expansion, a concise strategy combining rational cavity design, combinatorial active-site saturation test (CAST), and thermostability engineering was designed, that transformed the weakly active IR-G36 into a variant M5 with superior performance for the synthesis of (R)-3-benzylamino-1-Boc-piperidine, with a 4193-fold improvement in catalytic efficiency, a 16.2 °C improvement in T m , and a significant increase in the e.e. value from 78 % (R) to >99 % (R). M5 exhibits broad substrate scope for the synthesis of diverse azacycloalkylamines, and the reaction was demonstrated on a hectogram-scale under industrially relevant conditions. Our study provides a compelling example of the preparation of versatile and efficient IREDs, with exciting opportunities in medicinal and process chemistry as well as synthetic biology.


  • Organizational Affiliation
    • State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.

Macromolecule Content 

  • Total Structure Weight: 71.91 kDa 
  • Atom Count: 4,936 
  • Modeled Residue Count: 580 
  • Deposited Residue Count: 672 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
3-hydroxyisobutyrate dehydrogenase-like beta-hydroxyacid dehydrogenaseA [auth B],
B [auth A]
336Actinoalloteichus hymeniacidonisMutation(s): 0 
Gene Names: BKA25_002661

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free:  0.199 (Depositor), 0.198 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.523α = 90
b = 60.676β = 92.96
c = 91.396γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
RESOLVEphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)ChinaNSF:31872614

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-06
    Type: Initial release
  • Version 1.1: 2022-04-20
    Changes: Database references
  • Version 1.2: 2022-06-08
    Changes: Database references
  • Version 1.3: 2024-05-29
    Changes: Data collection