5G6S | pdb_00005g6s

Imine reductase from Aspergillus oryzae in complex with NADP(H) and (R)-rasagiline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.229 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

A reductive aminase from Aspergillus oryzae.

Aleku, G.A.France, S.P.Man, H.Mangas-Sanchez, J.Montgomery, S.L.Sharma, M.Leipold, F.Hussain, S.Grogan, G.Turner, N.J.

(2017) Nat Chem 9: 961-969

  • DOI: https://doi.org/10.1038/nchem.2782
  • Primary Citation Related Structures: 
    5G6R, 5G6S

  • PubMed Abstract: 

    Reductive amination is one of the most important methods for the synthesis of chiral amines. Here we report the discovery of an NADP(H)-dependent reductive aminase from Aspergillus oryzae (AspRedAm, Uniprot code Q2TW47) that can catalyse the reductive coupling of a broad set of carbonyl compounds with a variety of primary and secondary amines with up to >98% conversion and with up to >98% enantiomeric excess. In cases where both carbonyl and amine show high reactivity, it is possible to employ a 1:1 ratio of the substrates, forming amine products with up to 94% conversion. Steady-state kinetic studies establish that the enzyme is capable of catalysing imine formation as well as reduction. Crystal structures of AspRedAm in complex with NADP(H) and also with both NADP(H) and the pharmaceutical ingredient (R)-rasagiline are reported. We also demonstrate preparative scale reductive aminations with wild-type and Q240A variant biocatalysts displaying total turnover numbers of up to 32,000 and space time yields up to 3.73 g l -1  d -1 .


  • Organizational Affiliation
    • School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK.

Macromolecule Content 

  • Total Structure Weight: 256.79 kDa 
  • Atom Count: 17,882 
  • Modeled Residue Count: 2,309 
  • Deposited Residue Count: 2,360 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
IMINE REDUCTASE
A, B, C, D, E
A, B, C, D, E, F, G, H
295Aspergillus oryzaeMutation(s): 0 
EC: 1.5.1.48 (PDB Primary Data), 1.1.1 (UniProt)
UniProt
Find proteins for Q2TW47 (Aspergillus oryzae (strain ATCC 42149 / RIB 40))
Explore Q2TW47 
Go to UniProtKB:  Q2TW47
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2TW47
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP

Query on NDP



Download:Ideal Coordinates CCD File
I [auth A]
K [auth B]
M [auth C]
O [auth D]
Q [auth E]
I [auth A],
K [auth B],
M [auth C],
O [auth D],
Q [auth E],
S [auth F],
U [auth G],
W [auth H]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
RAU

Query on RAU



Download:Ideal Coordinates CCD File
J [auth A]
L [auth B]
N [auth C]
P [auth D]
R [auth E]
J [auth A],
L [auth B],
N [auth C],
P [auth D],
R [auth E],
T [auth F],
V [auth G],
X [auth H]
RASAGILINE
C12 H13 N
RUOKEQAAGRXIBM-GFCCVEGCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.229 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.822α = 108.75
b = 80.255β = 108.78
c = 123.895γ = 90.05
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2017-10-04
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description