6R4G

Crystal structure of human GFAT-1 in complex with UDP-GlcNAc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.501 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Loss of GFAT-1 feedback regulation activates the hexosamine pathway that modulates protein homeostasis.

Ruegenberg, S.Horn, M.Pichlo, C.Allmeroth, K.Baumann, U.Denzel, M.S.

(2020) Nat Commun 11: 687-687

  • DOI: 10.1038/s41467-020-14524-5
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glutamine fructose-6-phosphate amidotransferase (GFAT) is the key enzyme in the hexosamine pathway (HP) that produces uridine 5'-diphospho-N-acetyl-D-glucosamine (UDP-GlcNAc), linking energy metabolism with posttranslational protein glycosylation. In ...

    Glutamine fructose-6-phosphate amidotransferase (GFAT) is the key enzyme in the hexosamine pathway (HP) that produces uridine 5'-diphospho-N-acetyl-D-glucosamine (UDP-GlcNAc), linking energy metabolism with posttranslational protein glycosylation. In Caenorhabditis elegans, we previously identified gfat-1 gain-of-function mutations that elevate UDP-GlcNAc levels, improve protein homeostasis, and extend lifespan. GFAT is highly conserved, but the gain-of-function mechanism and its relevance in mammalian cells remained unclear. Here, we present the full-length crystal structure of human GFAT-1 in complex with various ligands and with important mutations. UDP-GlcNAc directly interacts with GFAT-1, inhibiting catalytic activity. The longevity-associated G451E variant shows drastically reduced sensitivity to UDP-GlcNAc inhibition in enzyme activity assays. Our structural and functional data point to a critical role of the interdomain linker in UDP-GlcNAc inhibition. In mammalian cells, the G451E variant potently activates the HP. Therefore, GFAT-1 gain-of-function through loss of feedback inhibition constitutes a potential target for the treatment of age-related proteinopathies.


    Organizational Affiliation

    CECAD-Cluster of Excellence, University of Cologne, 50931, Cologne, Germany. martin.denzel@age.mpg.de.,University of Cologne, Institute of Biochemistry, 50674, Cologne, Germany.,University of Cologne, Institute of Biochemistry, 50674, Cologne, Germany. ulrich.baumann@uni-koeln.de.,Max Planck Institute for Biology of Ageing, 50931, Cologne, Germany. martin.denzel@age.mpg.de.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Cologne, Germany. martin.denzel@age.mpg.de.,Max Planck Institute for Biology of Ageing, 50931, Cologne, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1
A, B
687Homo sapiensMutation(s): 0 
Gene Names: GFPT1 (GFAT, GFPT)
EC: 2.6.1.16
Find proteins for Q06210 (Homo sapiens)
Go to Gene View: GFPT1
Go to UniProtKB:  Q06210
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G6Q
Query on G6Q

Download SDF File 
Download CCD File 
A, B
GLUCOSE-6-PHOSPHATE
C6 H13 O9 P
VFRROHXSMXFLSN-SLPGGIOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
UD1
Query on UD1

Download SDF File 
Download CCD File 
A, B
URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
C17 H27 N3 O17 P2
LFTYTUAZOPRMMI-CFRASDGPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.501 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.190 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 152.432α = 90.00
b = 152.432β = 90.00
c = 169.268γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Federal Ministry for Education and ResearchGermany01GQ1423A
European CommissionGermanyERC-2014-StG-640254-MetAGEn

Revision History 

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2020-02-19
    Type: Database references