6SE3

Crystal Structure of Ancestral Flavin-containing monooxygenase (FMO) 3-6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Ancestral-sequence reconstruction unveils the structural basis of function in mammalian FMOs.

Nicoll, C.R.Bailleul, G.Fiorentini, F.Mascotti, M.L.Fraaije, M.W.Mattevi, A.

(2020) Nat Struct Mol Biol 27: 14-24

  • DOI: https://doi.org/10.1038/s41594-019-0347-2
  • Primary Citation of Related Structures:  
    6SE3, 6SEK, 6SEM, 6SF0

  • PubMed Abstract: 

    Flavin-containing monooxygenases (FMOs) are ubiquitous in all domains of life and metabolize a myriad of xenobiotics, including toxins, pesticides and drugs. However, despite their pharmacological importance, structural information remains bereft. To further our understanding behind their biochemistry and diversity, we used ancestral-sequence reconstruction, kinetic and crystallographic techniques to scrutinize three ancient mammalian FMOs: AncFMO2, AncFMO3-6 and AncFMO5. Remarkably, all AncFMOs could be crystallized and were structurally resolved between 2.7- and 3.2-Å resolution. These crystal structures depict the unprecedented topology of mammalian FMOs. Each employs extensive membrane-binding features and intricate substrate-profiling tunnel networks through a conspicuous membrane-adhering insertion. Furthermore, a glutamate-histidine switch is speculated to induce the distinctive Baeyer-Villiger oxidation activity of FMO5. The AncFMOs exhibited catalysis akin to human FMOs and, with sequence identities between 82% and 92%, represent excellent models. Our study demonstrates the power of ancestral-sequence reconstruction as a strategy for the crystallization of proteins.


  • Organizational Affiliation

    Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ancestral Flavin-containing monooxygenase (FMO) 3-6532synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
G [auth D]
J [auth A]
M [auth B]
P [auth C]
S [auth E]
G [auth D],
J [auth A],
M [auth B],
P [auth C],
S [auth E],
V [auth F]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
NAP
Query on NAP

Download Ideal Coordinates CCD File 
H [auth D]
K [auth A]
N [auth B]
Q [auth C]
T [auth E]
H [auth D],
K [auth A],
N [auth B],
Q [auth C],
T [auth E],
W [auth F]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
OXY
Query on OXY

Download Ideal Coordinates CCD File 
I [auth D]
L [auth A]
O [auth B]
R [auth C]
U [auth E]
I [auth D],
L [auth A],
O [auth B],
R [auth C],
U [auth E],
X [auth F]
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.089α = 90
b = 156.089β = 90
c = 370.605γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Commission722390

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Database references
  • Version 1.2: 2020-01-22
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description