7AV4

Dark state structure of the C432S mutant of Fatty Acid Photodecarboxylase (FAP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.175 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


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]654Chlorella variabilisMutation(s): 1 
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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.375α = 90
b = 104.683β = 90
c = 156.179γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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: 2024-01-31
    Changes: Refinement description