6TIE

Structure of A. niger Fdc I327S variant in complex with indol-2-carboxylic acid

  • Classification: LIGASE
  • Organism(s): Aspergillus niger
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2019-11-22 Released: 2020-06-24 
  • Deposition Author(s): Leys, D.
  • Funding Organization(s): Biotechnology and Biological Sciences Research Council, European Research Council

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.135 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Enzymatic C-H activation of aromatic compounds through CO 2 fixation.

Aleku, G.A.Saaret, A.Bradshaw-Allen, R.T.Derrington, S.R.Titchiner, G.R.Gostimskaya, I.Gahloth, D.Parker, D.A.Hay, S.Leys, D.

(2020) Nat Chem Biol 16: 1255-1260

  • DOI: https://doi.org/10.1038/s41589-020-0603-0
  • Primary Citation of Related Structures:  
    6TIB, 6TIC, 6TIE, 6TIH, 6TIJ, 6TIL, 6TIN, 6TIO

  • PubMed Abstract: 

    The direct C-H carboxylation of aromatic compounds is an attractive route to the corresponding carboxylic acids, but remains challenging under mild conditions. It has been proposed that the first step in anaerobic microbial degradation of recalcitrant aromatic compounds is a UbiD-mediated carboxylation. In this study, we use the UbiD enzyme ferulic acid decarboxylase (Fdc) in combination with a carboxylic acid reductase to create aromatic degradation-inspired cascade reactions, leading to efficient functionalization of styrene through CO 2 fixation. We reveal that rational structure-guided laboratory evolution can expand the substrate scope of Fdc, resulting in activity on a range of mono- and bicyclic aromatic compounds through a single mutation. Selected variants demonstrated 150-fold improvement in the conversion of coumarillic acid to benzofuran + CO 2 and unlocked reactivity towards naphthoic acid. Our data demonstrate that UbiD-mediated C-H activation is a versatile tool for the transformation of aryl/alkene compounds and CO 2 into commodity chemicals.


  • Organizational Affiliation

    Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, Manchester, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferulic acid decarboxylase 1A [auth AAA]507Aspergillus nigerMutation(s): 1 
Gene Names: FDC1ATCC64974_75990CAN33_0036860
EC: 4.1.1.102
UniProt
Find proteins for A0A3F3RNU4 (Aspergillus niger)
Explore A0A3F3RNU4 
Go to UniProtKB:  A0A3F3RNU4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3F3RNU4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BYN (Subject of Investigation/LOI)
Query on BYN

Download Ideal Coordinates CCD File 
E [auth AAA]hydroxylated prenyl-FMN
C22 H31 N4 O10 P
BDNVCRCOZIAGID-LWGWVAHUSA-N
ICB (Subject of Investigation/LOI)
Query on ICB

Download Ideal Coordinates CCD File 
F [auth AAA],
G [auth AAA]
1H-indole-2-carboxylic acid
C9 H7 N O2
HCUARRIEZVDMPT-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
B [auth AAA]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
C [auth AAA],
D [auth AAA]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.135 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.703α = 90
b = 63.798β = 90
c = 87.7γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2020-06-24 
  • Deposition Author(s): Leys, D.

Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/K017802
European Research CouncilUnited Kingdompre-FAB 695013

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-24
    Type: Initial release
  • Version 1.1: 2020-08-12
    Changes: Database references, Derived calculations, Refinement description
  • Version 1.2: 2020-09-30
    Changes: Database references
  • Version 1.3: 2020-10-28
    Changes: Database references
  • Version 1.4: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description