6SVM | pdb_00006svm

Crystal structure of human GFAT-1 in complex with Glucose-6-Phosphate, L-Glu, and UDP-GalNAc

• PDB DOI: https://doi.org/10.2210/pdb6SVM/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2019-09-18 Released: 2020-01-15 
• Deposition Author(s): Ruegenberg, S., Horn, M., Pichlo, C., Allmeroth, K., Baumann, U., Denzel, M.S.
• Funding Organization(s): German Federal Ministry for Education and Research, European Commission, European Union

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 
  0.222 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

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

• PubMed: 32019926 
• DOI: https://doi.org/10.1038/s41467-020-14524-5
• Primary Citation 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.

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Organizational Affiliation: 
• Max Planck Institute for Biology of Ageing, 50931, Cologne, Germany.
University of Cologne, Institute of Biochemistry, 50674, Cologne, Germany.
University of Cologne, Institute of Biochemistry, 50674, Cologne, Germany. [e-mail].
Max Planck Institute for Biology of Ageing, 50931, Cologne, Germany. [e-mail].
CECAD-Cluster of Excellence, University of Cologne, 50931, Cologne, Germany. [e-mail].
Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Cologne, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 157.32 kDa 
• Atom Count: 10,565 
• Modeled Residue Count: 1,315 
• Deposited Residue Count: 1,374 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1	A, B	687	Homo sapiens	Mutation(s): 0  Gene Names: GFPT1, GFAT, GFPT 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 GTEx:  ENSG00000198380

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UD2 (Subject of Investigation/LOI)	E [auth A], H [auth B]	URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE C17 H27 N3 O17 P2 LFTYTUAZOPRMMI-NESSUJCYSA-N
G6Q	C [auth A], G [auth B]	GLUCOSE-6-PHOSPHATE C6 H13 O9 P VFRROHXSMXFLSN-SLPGGIOYSA-N
GLU	D [auth A]	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N
MG	F [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free:  0.222 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.995	α = 90
b = 151.995	β = 90
c = 165.803	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-01-15 
Deposition Author(s): Ruegenberg, S., Horn, M., Pichlo, C., Allmeroth, K., Baumann, U., Denzel, M.S.

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Funding Organization	Location	Grant Number
German Federal Ministry for Education and Research	Germany	01GQ1423A
European Commission	Germany	ERC-2014-StG-640254-MetAGEn
European Union	Germany	iNEXT, Horizon 2020

Revision History  

• 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