8A8I

Xenobiotic reductase A from Pseudomonas putida in complex with ethyl (Z)-2-(hydroxyimino)-3-oxobutanoate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Mechanistic Insights into the Ene-Reductase-Catalyzed Promiscuous Reduction of Oximes to Amines.

Breukelaar, W.B.Polidori, N.Singh, A.Daniel, B.Glueck, S.M.Gruber, K.Kroutil, W.

(2023) ACS Catal 13: 2610-2618

  • DOI: https://doi.org/10.1021/acscatal.2c06137
  • Primary Citation of Related Structures:  
    8A8I, 8AU8, 8AU9, 8AUA, 8AUB, 8AUE, 8AUF, 8AUG, 8AUH, 8AUI, 8AUJ, 8AUL, 8AUM, 8AUN, 8AUO, 8AUQ

  • PubMed Abstract: 

    The biocatalytic reduction of the oxime moiety to the corresponding amine group has only recently been found to be a promiscuous activity of ene-reductases transforming α-oximo β-keto esters. However, the reaction pathway of this two-step reduction remained elusive. By studying the crystal structures of enzyme oxime complexes, analyzing molecular dynamics simulations, and investigating biocatalytic cascades and possible intermediates, we obtained evidence that the reaction proceeds via an imine intermediate and not via the hydroxylamine intermediate. The imine is reduced further by the ene-reductase to the amine product. Remarkably, a non-canonical tyrosine residue was found to contribute to the catalytic activity of the ene-reductase OPR3, protonating the hydroxyl group of the oxime in the first reduction step.


  • Organizational Affiliation

    Department of Chemistry, NAWI Graz, University of Graz, Heinrichstraße 28, 8010 Graz, Austria.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Xenobiotic reductaseA [auth B],
B [auth D]
371Pseudomonas putidaMutation(s): 0 
Gene Names: xenA
UniProt
Find proteins for Q9R9V9 (Pseudomonas putida)
Explore Q9R9V9 
Go to UniProtKB:  Q9R9V9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9R9V9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
C [auth B],
G [auth D]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
L9I (Subject of Investigation/LOI)
Query on L9I

Download Ideal Coordinates CCD File 
D [auth B],
H [auth D]
ethyl (2Z)-2-hydroxyimino-3-oxidanylidene-butanoate
C6 H9 N O4
IACSYDRIOYGJNH-ALCCZGGFSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
F [auth B],
I [auth D]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
MPD
Query on MPD

Download Ideal Coordinates CCD File 
E [auth B](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
J [auth D]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.149α = 90
b = 158.863β = 90
c = 49.672γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Science FundAustria--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-01
    Type: Initial release
  • Version 1.1: 2023-03-08
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description