9FM8 | pdb_00009fm8

Imine Reductase from Rhodococcus erythropolis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 
    0.300 (Depositor), 0.303 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery and Synthetic Applications of a NAD(P)H-Dependent Reductive Aminase from Rhodococcus erythropolis .

Jongkind, E.P.J.Domenech, J.Govers, A.van den Broek, M.Daran, J.M.Grogan, G.Paul, C.E.

(2025) ACS Catal 15: 211-219

  • DOI: https://doi.org/10.1021/acscatal.4c04935
  • Primary Citation of Related Structures:  
    9FM7, 9FM8

  • PubMed Abstract: 

    Reductive amination is one of the most synthetically direct routes to access chiral amines. Several Imine Reductases (IREDs) have been discovered to catalyze reductive amination (Reductive Aminases or RedAms), yet they are dependent on the expensive phosphorylated nicotinamide adenine dinucleotide cofactor NADPH and usually more active at basic pH. Here, we describe the discovery and synthetic potential of an IRED from Rhodococcus erythropolis ( Ryt RedAm) that catalyzes reductive amination between a series of medium to large carbonyl and amine compounds with conversions of up to >99% and 99% enantiomeric excess at neutral pH. Ryt RedAm catalyzes the formation of a substituted γ-lactam and N -methyl-1-phenylethanamine with stereochemistry opposite to that of fungal RedAms, giving the ( S )-enantiomer. This enzyme remarkably uses both NADPH and NADH cofactors with K M values of 15 and 247 μM and turnover numbers k cat of 3.6 and 9.0 s -1 , respectively, for the reductive amination of hexanal with allylamine. The crystal structure obtained provides insights into the flexibility to also accept NADH, with residues R35 and I69 diverging from that of other IREDs/RedAms in the otherwise conserved Rossmann fold. Ryt RedAm thus represents a subfamily of enzymes that enable synthetic applications using NADH-dependent reductive amination to access complementary chiral amine products.


  • Organizational Affiliation
    • Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)-dependent oxidoreductase291Rhodococcus erythropolisMutation(s): 0 
Gene Names: EHW12_26885
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: 2.38 Å
  • R-Value Free:  0.300 (Depositor), 0.303 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.66α = 90
b = 80.66β = 90
c = 82.78γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-25
    Type: Initial release
  • Version 1.1: 2025-01-22
    Changes: Database references