6ZMJ

Crystal structure of human GFAT-1 R203H


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

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This is version 1.1 of the entry. See complete history


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

  • DOI: 10.1038/s41467-021-22320-y
  • Primary Citation of 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 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.


    Related Citations: 
    • Protein kinase A controls the hexosamine pathway by tuning the feedback inhibition of GFAT-1
      Ruegenberg, S., Mayr, F., Miethe, S., Atanassov, I., Baumann, U., Denzel, M.S.
      (2020) Biorxiv --: --

    Organizational Affiliation

    Center for Molecular Medicine Cologne (CMMC), University of Cologne, 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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G6Q (Subject of Investigation/LOI)
Query on G6Q

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

Download Ideal Coordinates CCD File 
D [auth A]GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.766α = 90
b = 152.766β = 90
c = 164.81γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
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
German Research Foundation (DFG)GermanyINST 216/949-1 FUGG

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-05
    Type: Initial release
  • Version 1.1: 2021-04-28
    Changes: Database references