6YRZ

Crystal structure of FAP et pH 8.5 after illumination at 150K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.158 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

    Aix-Marseille University, CEA, CNRS, Institute of Biosciences and Biotechnologies, BIAM Cadarache, 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, chloroplasticA [auth AAA]578Chlorella variabilisMutation(s): 0 
Gene Names: FAPCHLNCDRAFT_28598
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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
B [auth AAA]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
STE
Query on STE

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E [auth AAA]STEARIC ACID
C18 H36 O2
QIQXTHQIDYTFRH-UHFFFAOYSA-N
PJ8 (Subject of Investigation/LOI)
Query on PJ8

Download Ideal Coordinates CCD File 
C [auth AAA]heptadecane
C17 H36
NDJKXXJCMXVBJW-UHFFFAOYSA-N
1PE
Query on 1PE

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F [auth AAA]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
CO2
Query on CO2

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D [auth AAA]CARBON DIOXIDE
C O2
CURLTUGMZLYLDI-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.47α = 90
b = 104.56β = 90
c = 156.9γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-18-CE11-0021

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-21
    Type: Initial release
  • Version 1.1: 2023-12-13
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2024-01-24
    Changes: Refinement description