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

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

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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: https://doi.org/10.1038/s41467-020-14524-5
  • Primary Citation of Related Structures:  
    6R4E, 6R4F, 6R4G, 6R4H, 6R4I, 6R4J, 6SVM, 6SVO, 6SVP, 6SVQ

  • 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 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

    Max Planck Institute for Biology of Ageing, 50931, Cologne, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1
A, B
687Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q06210 (Homo sapiens)
Explore Q06210 
Go to UniProtKB:  Q06210
PHAROS:  Q06210
GTEx:  ENSG00000198380 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06210
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.432α = 90
b = 152.432β = 90
c = 169.268γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description