Biological Assembly 1  

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 398.53 kDa 
• Atom Count: 27,918 
• Modelled Residue Count: 3,476 
• Deposited Residue Count: 3,606 
• Unique protein chains: 1

 6U0S

Crystal structure of the flavin-dependent monooxygenase PieE in complex with FAD and substrate

• PDB DOI:  https://doi.org/10.2210/pdb6U0S/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Streptomyces marincola
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-08-14 Released: 2020-03-11 
• Deposition Author(s): Shi, R., Manenda, M.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 0.239 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

Literature

Structural analyses of the Group A flavin-dependent monooxygenase PieE reveal a sliding FAD cofactor conformation bridging OUT and IN conformations.

Manenda, M.S., Picard, M.E., Zhang, L., Cyr, N., Zhu, X., Barma, J., Pascal, J.M., Couture, M., Zhang, C., Shi, R.

(2020) J Biol Chem 295: 4709-4722

• PubMed: 32111738 
• DOI: https://doi.org/10.1074/jbc.RA119.011212
• Primary Citation of Related Structures:  
  6U0P, 6U0S


• PubMed Abstract: 
  

Group A flavin-dependent monooxygenases catalyze the cleavage of the oxygen-oxygen bond of dioxygen, followed by the incorporation of one oxygen atom into the substrate molecule with the aid of NADPH and FAD. These flavoenzymes play an important role in many biological processes, and their most distinct structural feature is the choreographed motions of flavin, which typically adopts two distinct conformations (OUT and IN) to fulfill its function. Notably, these enzymes seem to have evolved a delicate control system to avoid the futile cycle of NADPH oxidation and FAD reduction in the absence of substrate, but the molecular basis of this system remains elusive. Using protein crystallography, size-exclusion chromatography coupled to multi-angle light scattering (SEC-MALS), and small-angle X-ray scattering (SEC-SAXS) and activity assay, we report here a structural and biochemical characterization of PieE, a member of the Group A flavin-dependent monooxygenases involved in the biosynthesis of the antibiotic piericidin A1. This analysis revealed that PieE forms a unique hexamer. Moreover, we found, to the best of our knowledge for the first time, that in addition to the classical OUT and IN conformations, FAD possesses a "sliding" conformation that exists in between the OUT and IN conformations. This observation sheds light on the underlying mechanism of how the signal of substrate binding is transmitted to the FAD-binding site to efficiently initiate NADPH binding and FAD reduction. Our findings bridge a gap currently missing in the orchestrated order of chemical events catalyzed by this important class of enzymes.

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Organizational Affiliation: 

Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,4-dichlorophenol 6-monooxygenase	A, B, C, D, E, F	601	Streptomyces marincola	Mutation(s): 0  Gene Names: CAG99_26330
UniProt
Find proteins for W0C4C9 (Streptomyces marincola) Explore W0C4C9  Go to UniProtKB:  W0C4C9

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	AA [auth D], G [auth A], GA [auth E], O [auth B], OA [auth F], U [auth C]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
PKS (Subject of Investigation/LOI)	CA [auth D], I [auth A], IA [auth E], Q [auth B], QA [auth F], V [auth C]	2-[(2E,5E,7E,9R,10R,11E)-10-hydroxy-3,7,9,11-tetramethyltrideca-2,5,7,11-tetraen-1-yl]-6-methoxy-3-methylpyridin-4-ol C24 H35 N O3 RESCEXRHBPSAAM-HWMDAMIQSA-N
1PE	DA [auth D], K [auth A], KA [auth E], R [auth B], RA [auth F], X [auth C]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PGE	J [auth A], JA [auth E], T [auth C], W [auth C]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL	FA [auth D], M [auth A], MA [auth E], N [auth A], NA [auth E], Z [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	BA [auth D], EA [auth D], H [auth A], HA [auth E], L [auth A], LA [auth E], P [auth B], PA [auth F], S [auth B], SA [auth F], Y [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 0.239 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.339	α = 90
b = 187.129	β = 90
c = 239.089	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-03-11 
Deposition Author(s): Shi, R., Manenda, M.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	436202

Revision History  

• Version 1.0: 2020-03-11
  Type: Initial release
  
• Version 1.1: 2020-04-15
  Changes: Database references