6TIO

Structure of A. niger Fdc Wt in complex with FMN and benzothiophene 2 carboxylic acid

  • Classification: LIGASE
  • Organism(s): Aspergillus niger
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • 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: 1.54 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.148 

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]508Aspergillus nigerMutation(s): 0 
Gene Names: fdc1An03g06590
EC: 4.1.1.102
UniProt
Find proteins for A2QHE5 (Aspergillus niger (strain ATCC MYA-4892 / CBS 513.88 / FGSC A1513))
Explore A2QHE5 
Go to UniProtKB:  A2QHE5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2QHE5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
E [auth AAA]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
ND8 (Subject of Investigation/LOI)
Query on ND8

Download Ideal Coordinates CCD File 
F [auth AAA]benzothiophene 2 carboxylic acid
C9 H6 O2 S
DYSJMQABFPKAQM-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: 1.54 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.148 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.39α = 90
b = 63.283β = 90
c = 87.501γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling

Structure Validation

View Full Validation Report



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
  • 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