6TIN | pdb_00006tin

Structure of A. niger Fdc WT in complex with FMN and indole 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: 1.28 Å
  • R-Value Free: 
    0.198 (Depositor), 0.198 (DCC) 
  • R-Value Work: 
    0.160 (Depositor), 0.160 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6TIN

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 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.

Macromolecule Content 

  • Total Structure Weight: 57.09 kDa 
  • Atom Count: 4,580 
  • Modeled Residue Count: 497 
  • Deposited Residue Count: 508 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
ICB
(Subject of Investigation/LOI)

Query on ICB



Download:Ideal Coordinates CCD File
F [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: 1.28 Å
  • R-Value Free:  0.198 (Depositor), 0.198 (DCC) 
  • R-Value Work:  0.160 (Depositor), 0.160 (DCC) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.894α = 90
b = 63.934β = 90
c = 87.668γ = 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