6U0S

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


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 

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Ligand Structure Quality Assessment 


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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

  • DOI: 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2,4-dichlorophenol 6-monooxygenaseA, B, C, D, E, F601Streptomyces sp. SCSIO 3032Mutation(s): 0 
Gene Names: CAG99_26330
UniProt
Find proteins for W0C4C9 (Streptomyces sp. SCSIO 3032)
Explore W0C4C9 
Go to UniProtKB:  W0C4C9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
PKS (Subject of Investigation/LOI)
Query on PKS

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
J [auth A], JA [auth E], T [auth C], W [auth C]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
BA [auth D] , EA [auth D] , H [auth A] , HA [auth E] , L [auth A] , LA [auth E] , P [auth B] , PA [auth F] , 
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
 Ligand Interaction
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 = 91.339α = 90
b = 187.129β = 90
c = 239.089γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-08-14 
  • Released Date: 2020-03-11 
  • Deposition Author(s): Shi, R., Manenda, M.

Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada436202

Revision History  (Full details and data files)

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