5N6G | pdb_00005n6g

NerA from Agrobacterium radiobacter in complex with 2-phenylacrylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 
    0.164 (Depositor), 0.170 (DCC) 
  • R-Value Work: 
    0.140 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.142 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FMNClick on this verticalbar to view details

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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTN Reductase379Agrobacterium tumefaciensMutation(s): 0 
Gene Names: nerA
UniProt
Find proteins for O31246 (Rhizobium radiobacter)
Explore O31246 
Go to UniProtKB:  O31246
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO31246
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
8OZ
Query on 8OZ

Download Ideal Coordinates CCD File 
C [auth A]2-Phenylacrylic acid
C9 H8 O2
ONPJWQSDZCGSQM-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
J [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free:  0.164 (Depositor), 0.170 (DCC) 
  • R-Value Work:  0.140 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.142 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.09α = 90
b = 69.16β = 90
c = 91.89γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FMNClick on this verticalbar to view details

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