5N6Q | pdb_00005n6q

Xenobiotic reductase A (XenA) from Pseudomonas putida in complex with 2-phenylacrylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.225 (Depositor), 0.226 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 
    0.169 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5N6Q

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structural insights into the ene-reductase synthesis of profens.

Waller, J.Toogood, H.S.Karuppiah, V.Rattray, N.J.W.Mansell, D.J.Leys, D.Gardiner, J.M.Fryszkowska, A.Ahmed, S.T.Bandichhor, R.Reddy, G.P.Scrutton, N.S.

(2017) Org Biomol Chem 15: 4440-4448

  • DOI: https://doi.org/10.1039/c7ob00163k
  • Primary Citation Related Structures: 
    5N6G, 5N6Q

  • PubMed Abstract: 

    Reduction of double bonds of α,β-unsaturated carboxylic acids and esters by ene-reductases remains challenging and it typically requires activation by a second electron-withdrawing moiety, such as a halide or second carboxylate group. We showed that profen precursors, 2-arylpropenoic acids and their esters, were efficiently reduced by Old Yellow Enzymes (OYEs). The XenA and GYE enzymes showed activity towards acids, while a wider range of enzymes were active towards the equivalent methyl esters. Comparative co-crystal structural analysis of profen-bound OYEs highlighted key interactions important in determining substrate binding in a catalytically active conformation. The general utility of ene reductases for the synthesis of (R)-profens was established and this work will now drive future mutagenesis studies to screen for the production of pharmaceutically-active (S)-profens.


  • Organizational Affiliation
    • Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK. nigel.scrutton@manchester.ac.uk.

Macromolecule Content 

  • Total Structure Weight: 83.42 kDa 
  • Atom Count: 6,171 
  • Modeled Residue Count: 713 
  • Deposited Residue Count: 742 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NADH:flavin oxidoreductase
A, B
371Pseudomonas putidaMutation(s): 0 
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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN

Query on FMN



Download:Ideal Coordinates CCD File
H [auth A],
I [auth B]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
8OZ

Query on 8OZ



Download:Ideal Coordinates CCD File
C [auth A],
J [auth B]
2-Phenylacrylic acid
C9 H8 O2
ONPJWQSDZCGSQM-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
G [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
K [auth B]
L [auth B]
D [auth A],
E [auth A],
F [auth A],
K [auth B],
L [auth B],
M [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.225 (Depositor), 0.226 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 0.169 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.391α = 90
b = 84.041β = 90
c = 155.97γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/I015779/1

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2017-05-31
    Changes: Database references
  • Version 1.2: 2017-08-30
    Changes: Author supporting evidence
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description