6YRV

Crystal structure of FAP after illumination at 100K

• PDB DOI:  https://doi.org/10.2210/pdb6YRV/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Chlorella variabilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-04-20 Released: 2021-04-21 
• Deposition Author(s): Sorigue, D., Gotthard, G., Blangy, S., Nurizzo, D., Royant, A., Beisson, F., Arnoux, P.
• Funding Organization(s): French National Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.203 
• R-Value Work: 0.165 

Literature

Mechanism and dynamics of fatty acid photodecarboxylase.

Sorigue, D., Hadjidemetriou, K., Blangy, S., Gotthard, G., Bonvalet, A., Coquelle, N., Samire, P., Aleksandrov, A., Antonucci, L., Benachir, A., Boutet, S., Byrdin, M., Cammarata, M., Carbajo, S., Cuine, S., Doak, R.B., Foucar, L., Gorel, A., Grunbein, M., Hartmann, E., Hienerwadel, R., Hilpert, M., Kloos, M., Lane, T.J., Legeret, B., Legrand, P., Li-Beisson, Y., Moulin, S.L.Y., Nurizzo, D., Peltier, G., Schiro, G., Shoeman, R.L., Sliwa, M., Solinas, X., Zhuang, B., Barends, T.R.M., Colletier, J.P., Joffre, M., Royant, A., Berthomieu, C., Weik, M., Domratcheva, T., Brettel, K., Vos, M.H., Schlichting, I., Arnoux, P., Muller, P., Beisson, F.

(2021) Science 372

• PubMed: 33833098 
• DOI: https://doi.org/10.1126/science.abd5687
• Primary Citation of Related Structures:  
  6YRU, 6YRV, 6YRX, 6YRZ, 6YS1, 6YS2, 6ZH7, 7AV4


• PubMed Abstract: 
  

Fatty acid photodecarboxylase (FAP) is a photoenzyme with potential green chemistry applications. By combining static, time-resolved, and cryotrapping spectroscopy and crystallography as well as computation, we characterized Chlorella variabilis FAP reaction intermediates on time scales from subpicoseconds to milliseconds. High-resolution crystal structures from synchrotron and free electron laser x-ray sources highlighted an unusual bent shape of the oxidized flavin chromophore. We demonstrate that decarboxylation occurs directly upon reduction of the excited flavin by the fatty acid substrate. Along with flavin reoxidation by the alkyl radical intermediate, a major fraction of the cleaved carbon dioxide unexpectedly transformed in 100 nanoseconds, most likely into bicarbonate. This reaction is orders of magnitude faster than in solution. Two strictly conserved residues, R451 and C432, are essential for substrate stabilization and functional charge transfer.

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Organizational Affiliation: 

Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 13108 Saint-Paul-lez-Durance, France. [e-mail] [e-mail] [e-mail] [e-mail] [e-mail] [e-mail] [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 62.44 kDa 
• Atom Count: 4,884 
• Modelled Residue Count: 573 
• Deposited Residue Count: 578 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty acid Photodecarboxylase	A [auth AAA]	578	Chlorella variabilis	Mutation(s): 0  Gene Names: FAP, CHLNCDRAFT_28598 EC: 4.1.1.106
UniProt
Find proteins for A0A248QE08 (Chlorella variabilis) Explore A0A248QE08  Go to UniProtKB:  A0A248QE08

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth AAA]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
STE	E [auth AAA]	STEARIC ACID C18 H36 O2 QIQXTHQIDYTFRH-UHFFFAOYSA-N
PJ8 (Subject of Investigation/LOI)	C [auth AAA]	heptadecane C17 H36 NDJKXXJCMXVBJW-UHFFFAOYSA-N
CO2	D [auth AAA]	CARBON DIOXIDE C O2 CURLTUGMZLYLDI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.203 
• R-Value Work: 0.165 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.96	α = 90
b = 103.86	β = 90
c = 156.3	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-04-21 
Deposition Author(s): Sorigue, D., Gotthard, G., Blangy, S., Nurizzo, D., Royant, A., Beisson, F., Arnoux, P.

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Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-18-CE11-0021

Revision History  

• Version 1.0: 2021-04-21
  Type: Initial release