9R79 | pdb_00009r79

Imine Reductase IR91 from Kribbella flavida with NADP+ and 5-methoxy-2-tetralone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.239 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Structures of "Tyrosine-IRED" IR91 from Kribbella flavida in Complex with a Reductive Amination Substrate and Product.

Srinivas, K.Gilio, A.K.Sharma, M.Green, L.Ascham, A.Domenech, J.Pogranyi, B.Li, J.France, S.P.Lewis, R.D.Unsworth, W.P.Grogan, G.

(2025) Chembiochem 26: e202500450-e202500450

  • DOI: https://doi.org/10.1002/cbic.202500450
  • Primary Citation Related Structures: 
    9R76, 9R79, 9R7A

  • PubMed Abstract: 

    Imine reductases with an (S)-preference for the reduction of the model substrate 2-methyl pyrroline typically contain tyrosine in the active site (Y-IREDs) instead of the aspartate present within (R)-selective enzymes (D-IREDs). As with D-IREDs, a subset of Y-IREDs is capable of enabling reductive amination reactions between some ketone and amine partners to give optically active amines with high optical purity. However, structures of Y-IREDs in complex with the substrates and products of the reductive amination have not been forthcoming. Herein, structures of the Y-IRED IR91 from Kribbella flavida in complex with 5-methoxy-2-tetralone, a synthetic precursor to the anti-Parkinson's treatment rotigotine, and also its reductive amination product with methylamine, 5-methoxy-(S)-2-(N-methylamino)-tetralin, are presented. The structures, in combination with mutation and kinetic studies, support a role for tryptophan residue W258 in the activity of the enzyme, possibly in binding of the ketone prior to reaction with methylamine.


  • Organizational Affiliation
    • Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.

Macromolecule Content 

  • Total Structure Weight: 64.43 kDa 
  • Atom Count: 4,782 
  • Modeled Residue Count: 582 
  • Deposited Residue Count: 592 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
6-phosphogluconate dehydrogenase NAD-binding protein
A, B
296Kribbella flavidaMutation(s): 0 
Gene Names: Kfla_3935
UniProt
Find proteins for D2PR38 (Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399))
Explore D2PR38 
Go to UniProtKB:  D2PR38
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2PR38
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
(Subject of Investigation/LOI)

Query on NAP



Download:Ideal Coordinates CCD File
F [auth A],
L [auth B]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
A1JDH
(Subject of Investigation/LOI)

Query on A1JDH



Download:Ideal Coordinates CCD File
G [auth A],
M [auth B]
5-methoxy-3,4-dihydro-1~{H}-naphthalen-2-one
C11 H12 O2
MDAIAXRTLTVEOU-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
I [auth B]
J [auth B]
C [auth A],
D [auth A],
E [auth A],
I [auth B],
J [auth B],
K [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
H [auth A],
N [auth B],
O [auth B],
P [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.239 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.9α = 90
b = 102.89β = 90
c = 108.7γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-05
    Type: Initial release