6YS1

Crystal structure of FAP R451K mutant in the dark at 100K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.0 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: 10.1126/science.abd5687
  • Primary Citation of Related Structures:  
    7AV4, 6ZH7, 6YRX, 6YRZ, 6YS1, 6YS2, 6YRV, 6YRU

  • 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 ...

    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. frederic.beisson@cea.fr pavel.muller@i2bc.paris-saclay.fr pascal.arnoux@cea.fr Ilme.schlichting@mpimf-heidelberg.mpg.de marten.vos@polytechnique.edu tatjana.domratcheva@mpimf-heidelberg.mpg.de martin.weik@ibs.fr catherine.berthomieu@cea.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fatty acid PhotodecarboxylaseA [auth AAA]578Chlorella 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

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

Download Ideal Coordinates CCD File 
B [auth AAA], C [auth AAA]STEARIC ACID
C18 H36 O2
QIQXTHQIDYTFRH-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
E [auth AAA]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.166 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.62α = 90
b = 102.78β = 90
c = 155.83γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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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