5NCC

Structure of Fatty acid Photodecarboxylase in complex with FAD and palmitic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.229 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

An algal photoenzyme converts fatty acids to hydrocarbons.

Sorigue, D.Legeret, B.Cuine, S.Blangy, S.Moulin, S.Billon, E.Richaud, P.Brugiere, S.Coute, Y.Nurizzo, D.Muller, P.Brettel, K.Pignol, D.Arnoux, P.Li-Beisson, Y.Peltier, G.Beisson, F.

(2017) Science 357: 903-907

  • DOI: https://doi.org/10.1126/science.aan6349
  • Primary Citation of Related Structures:  
    5NCC

  • PubMed Abstract: 

    Although many organisms capture or respond to sunlight, few enzymes are known to be driven by light. Among these are DNA photolyases and the photosynthetic reaction centers. Here, we show that the microalga Chlorella variabilis NC64A harbors a photoenzyme that acts in lipid metabolism. This enzyme belongs to an algae-specific clade of the glucose-methanol-choline oxidoreductase family and catalyzes the decarboxylation of free fatty acids to n-alkanes or -alkenes in response to blue light. Crystal structure of the protein reveals a fatty acid-binding site in a hydrophobic tunnel leading to the light-capturing flavin adenine dinucleotide (FAD) cofactor. The decarboxylation is initiated through electron abstraction from the fatty acid by the photoexcited FAD with a quantum yield >80%. This photoenzyme, which we name fatty acid photodecarboxylase, may be useful in light-driven, bio-based production of hydrocarbons.


  • Organizational Affiliation

    Biosciences and Biotechnologies Institute of Aix-Marseille (BIAM), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), CNRS and Aix-Marseille University, UMR 7265 LB3M, CEA Cadarache, F-13108, Saint-Paul-lez-Durance, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fatty acid Photodecarboxylase
A, B, C, D, E
A, B, C, D, E, F
594Chlorella variabilisMutation(s): 0 
EC: 4.1.1.106
UniProt
Find proteins for A0A248QE08 (Chlorella variabilis)
Explore A0A248QE08 
Go to UniProtKB:  A0A248QE08
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A248QE08
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
K [auth C]
M [auth D]
O [auth E]
G [auth A],
I [auth B],
K [auth C],
M [auth D],
O [auth E],
P [auth F]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
PLM
Query on PLM

Download Ideal Coordinates CCD File 
H [auth A],
J [auth B],
L [auth C],
N [auth D]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.234α = 90
b = 192.109β = 113.28
c = 116.127γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
BALBESphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Database references
  • Version 1.2: 2019-06-12
    Changes: Data collection, Structure summary
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description