7NF0

T. atroviride Fdc variant TaFdcV in complex with hydroxylated prFMN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Directed evolution of prenylated FMN-dependent Fdc supports efficient in vivo isobutene production.

Saaret, A.Villiers, B.Stricher, F.Anissimova, M.Cadillon, M.Spiess, R.Hay, S.Leys, D.

(2021) Nat Commun 12: 5300-5300

  • DOI: https://doi.org/10.1038/s41467-021-25598-0
  • Primary Citation of Related Structures:  
    7NEY, 7NF0, 7NF1, 7NF2, 7NF3, 7NF4

  • PubMed Abstract: 

    Isobutene is a high value gaseous alkene used as fuel additive and a chemical building block. As an alternative to fossil fuel derived isobutene, we here develop a modified mevalonate pathway for the production of isobutene from glucose in vivo. The final step in the pathway consists of the decarboxylation of 3-methylcrotonic acid, catalysed by an evolved ferulic acid decarboxylase (Fdc) enzyme. Fdc belongs to the prFMN-dependent UbiD enzyme family that catalyses reversible decarboxylation of (hetero)aromatic acids or acrylic acids with extended conjugation. Following a screen of an Fdc library for inherent 3-methylcrotonic acid decarboxylase activity, directed evolution yields variants with up to an 80-fold increase in activity. Crystal structures of the evolved variants reveal that changes in the substrate binding pocket are responsible for increased selectivity. Solution and computational studies suggest that isobutene cycloelimination is rate limiting and strictly dependent on presence of the 3-methyl group.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferulic acid decarboxylase 1
A, B
519Trichoderma atroviride IMI 206040Mutation(s): 11 
Gene Names: FDC1TRIATDRAFT_53567
EC: 4.1.1.102
UniProt
Find proteins for G9NLP8 (Hypocrea atroviridis (strain ATCC 20476 / IMI 206040))
Explore G9NLP8 
Go to UniProtKB:  G9NLP8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG9NLP8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BYN (Subject of Investigation/LOI)
Query on BYN

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
hydroxylated prenyl-FMN
C22 H31 N4 O10 P
BDNVCRCOZIAGID-LWGWVAHUSA-N
NO3
Query on NO3

Download Ideal Coordinates CCD File 
C [auth A]NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
H [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
MN
Query on MN

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

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
J [auth B],
K [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.593α = 90
b = 74.593β = 90
c = 345.772γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)United Kingdom695013

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-04
    Type: Initial release
  • Version 1.1: 2021-10-06
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description