6ZMJ | pdb_00006zmj

Crystal structure of human GFAT-1 R203H

• PDB DOI: https://doi.org/10.2210/pdb6ZMJ/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2020-07-02 Released: 2020-08-05 
• Deposition Author(s): Ruegenberg, S., Mayr, F., Miethe, S., Atanassov, I., Baumann, U., Denzel, M.S.
• Funding Organization(s): German Federal Ministry for Education and Research, European Commission, German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free: 
  0.239 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Protein kinase A controls the hexosamine pathway by tuning the feedback inhibition of GFAT-1.

Ruegenberg, S., Mayr, F.A.M.C., Atanassov, I., Baumann, U., Denzel, M.S.

(2021) Nat Commun 12: 2176-2176

• PubMed: 33846315 
• DOI: https://doi.org/10.1038/s41467-021-22320-y
• Primary Citation Related Structures: 
  6ZMJ, 6ZMK, 7NDL


• PubMed Abstract: 
  

  The hexosamine pathway (HP) is a key anabolic pathway whose product uridine 5'-diphospho-N-acetyl-D-glucosamine (UDP-GlcNAc) is an essential precursor for glycosylation processes in mammals. It modulates the ER stress response and HP activation extends lifespan in Caenorhabditis elegans. The highly conserved glutamine fructose-6-phosphate amidotransferase 1 (GFAT-1) is the rate-limiting HP enzyme. GFAT-1 activity is modulated by UDP-GlcNAc feedback inhibition and via phosphorylation by protein kinase A (PKA). Molecular consequences of GFAT-1 phosphorylation, however, remain poorly understood. Here, we identify the GFAT-1 R203H substitution that elevates UDP-GlcNAc levels in C. elegans. In human GFAT-1, the R203H substitution interferes with UDP-GlcNAc inhibition and with PKA-mediated Ser205 phosphorylation. Our data indicate that phosphorylation affects the interactions of the two GFAT-1 domains to control catalytic activity. Notably, Ser205 phosphorylation has two discernible effects: it lowers baseline GFAT-1 activity and abolishes UDP-GlcNAc feedback inhibition. PKA controls the HP by uncoupling the metabolic feedback loop of GFAT-1.

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Organizational Affiliation: 
• Max Planck Institute for Biology of Ageing, Cologne, Germany.
Institute of Biochemistry, University of Cologne, Cologne, Germany.
Max Planck Institute for Biology of Ageing, Cologne, Germany. [e-mail].
CECAD - Cluster of Excellence, University of Cologne, Cologne, Germany. [e-mail].
Center for Molecular Medicine Cologne (CMMC), University of Cologne, 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: 156.02 kDa 
• Atom Count: 10,329 
• Modeled Residue Count: 1,298 
• 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): 1  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G6Q	C [auth A], E [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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free:  0.239 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.766	α = 90
b = 152.766	β = 90
c = 164.81	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: 2020-08-05 
Deposition Author(s): Ruegenberg, S., Mayr, F., Miethe, S., Atanassov, I., 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
German Research Foundation (DFG)	Germany	INST 216/949-1 FUGG

Revision History  

• Version 1.0: 2020-08-05
  Type: Initial release
  
• Version 1.1: 2021-04-28
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Database references, Refinement description