6YRU

Crystal structure of FAP in the dark at 100K

PDB DOI: https://doi.org/10.2210/pdb6YRU/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.202
R-Value Work: 0.172

Starting Model: experimental
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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

PubMed: 33833098 Search on PubMed
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.

Macromolecule Content

Total Structure Weight: 62.44 kDa
Atom Count: 4,885
Modelled Residue Count: 573
Deposited Residue Count: 578
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty acid Photodecarboxylase	A [auth AAA]	578	Chlorella variabilis	Mutation(s): 0 EC: 4.1.1.106
UniProt
Find proteins for A0A248QE08 (Chlorella variabilis) Explore A0A248QE08 Go to UniProtKB: A0A248QE08
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A248QE08
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download Ideal Coordinates CCD File SDF format, chain D [auth AAA] MOL2 format, chain D [auth AAA] mmCIF format, chain D [auth AAA]	D [auth AAA]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain D [auth AAA] Interactions & Density Focus chain D [auth AAA]
STE (Subject of Investigation/LOI) Query on STE Download Ideal Coordinates CCD File SDF format, chain B [auth AAA] SDF format, chain C [auth AAA] MOL2 format, chain B [auth AAA] MOL2 format, chain C [auth AAA] mmCIF format, chain B [auth AAA] mmCIF format, chain C [auth AAA]	B [auth AAA], C [auth AAA]	STEARIC ACID C₁₈ H₃₆ O₂ QIQXTHQIDYTFRH-UHFFFAOYSA-N		Interactions Focus chain B [auth AAA] Focus chain C [auth AAA] Interactions & Density Focus chain B [auth AAA] Focus chain C [auth AAA]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.202
R-Value Work: 0.172
Space Group: I 2 2 2
Diffraction Data: https://doi.org/10.11577/1775333

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.69	α = 90
b = 103.57	β = 90
c = 155.95	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-04-21

Deposition Author(s):

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