8AUF

XenA Y183F variant in complex with ethyl (Z)-2-(hydroxyimino)-3-oxopentanoate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.148 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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
NADH:flavin oxidoreductase
A, B
371Pseudomonas putidaMutation(s): 1 
Gene Names: xenAHB4184_21910
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
O8I (Subject of Investigation/LOI)
Query on O8I

Download Ideal Coordinates CCD File 
C [auth A],
F [auth A],
H [auth B]
ethyl (2~{Z})-2-hydroxyimino-3-oxidanylidene-pentanoate
C7 H11 N O4
FOGXVRUMMPWXRL-VURMDHGXSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
E [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.148 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.35α = 90
b = 158.69β = 90
c = 57.38γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction
AutoProcessdata processing

Structure Validation

View Full Validation Report



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