6R4J

Crystal structure of human GFAT-1 G451E in complex with UDP-GlcNAc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

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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:  
    6R4I, 6R4H, 6R4J, 6R4E, 6R4G, 6R4F, 6SVQ, 6SVM, 6SVP, 6SVO

  • 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 ...

    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

    Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Cologne, Germany. martin.denzel@age.mpg.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1A, B687Homo sapiensMutation(s): 1 
Gene Names: GFPT1GFATGFPT
EC: 2.6.1.16
UniProt & NIH Common Fund Data Resources
Find proteins for Q06210 (Homo sapiens)
Explore Q06210 
Go to UniProtKB:  Q06210
PHAROS:  Q06210
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UD1 (Subject of Investigation/LOI)
Query on UD1

Download Ideal Coordinates CCD File 
C [auth A], G [auth B]URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
C17 H27 N3 O17 P2
LFTYTUAZOPRMMI-CFRASDGPSA-N
 Ligand Interaction
G6Q (Subject of Investigation/LOI)
Query on G6Q

Download Ideal Coordinates CCD File 
E [auth A], I [auth B]GLUCOSE-6-PHOSPHATE
C6 H13 O9 P
VFRROHXSMXFLSN-SLPGGIOYSA-N
 Ligand Interaction
GLU
Query on GLU

Download Ideal Coordinates CCD File 
F [auth A]GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A], H [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.227α = 90
b = 153.227β = 90
c = 162.544γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

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