3LFM

Crystal structure of the fat mass and obesity associated (FTO) protein reveals basis for its substrate specificity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the FTO protein reveals basis for its substrate specificity

Han, Z.Niu, T.Chang, J.Lei, X.Zhao, M.Wang, Q.Cheng, W.Wang, J.Feng, Y.Chai, J.

(2010) Nature 464: 1205-1209

  • DOI: 10.1038/nature08921

  • PubMed Abstract: 
  • Recent studies have unequivocally associated the fat mass and obesity-associated (FTO) gene with the risk of obesity. In vitro FTO protein is an AlkB-like DNA/RNA demethylase with a strong preference for 3-methylthymidine (3-meT) in single-stranded D ...

    Recent studies have unequivocally associated the fat mass and obesity-associated (FTO) gene with the risk of obesity. In vitro FTO protein is an AlkB-like DNA/RNA demethylase with a strong preference for 3-methylthymidine (3-meT) in single-stranded DNA or 3-methyluracil (3-meU) in single-stranded RNA. Here we report the crystal structure of FTO in complex with the mononucleotide 3-meT. FTO comprises an amino-terminal AlkB-like domain and a carboxy-terminal domain with a novel fold. Biochemical assays show that these two domains interact with each other, which is required for FTO catalytic activity. In contrast with the structures of other AlkB members, FTO possesses an extra loop covering one side of the conserved jelly-roll motif. Structural comparison shows that this loop selectively competes with the unmethylated strand of the DNA duplex for binding to FTO, suggesting that it has an important role in FTO selection against double-stranded nucleic acids. The ability of FTO to distinguish 3-meT or 3-meU from other nucleotides is conferred by its hydrogen-bonding interaction with the two carbonyl oxygen atoms in 3-meT or 3-meU. Taken together, these results provide a structural basis for understanding FTO substrate-specificity, and serve as a foundation for the rational design of FTO inhibitors.


    Organizational Affiliation

    National Institute of Biological Sciences, No. 7 Science Park Road, Beijing 102206, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein fto
A
495Homo sapiensMutation(s): 0 
Gene Names: FTO (KIAA1752)
Find proteins for Q9C0B1 (Homo sapiens)
Go to Gene View: FTO
Go to UniProtKB:  Q9C0B1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE2
Query on FE2

Download SDF File 
Download CCD File 
A
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
3DT
Query on 3DT

Download SDF File 
Download CCD File 
A
3-methylthymidine
C11 H16 N2 O5
JCVDICFLPGDHAT-DJLDLDEBSA-N
 Ligand Interaction
OGA
Query on OGA

Download SDF File 
Download CCD File 
A
N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
OGAIC50: 44000 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.239 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 142.860α = 90.00
b = 142.860β = 90.00
c = 83.800γ = 120.00
Software Package:
Software NamePurpose
SOLVEphasing
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-01-18 
  • Released Date: 2010-04-07 
  • Deposition Author(s): Chai, J., Han, Z.

Revision History 

  • Version 1.0: 2010-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance