6S24

Crystal structure of the TgGalNAc-T3 in complex with UDP, manganese and the peptide 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular basis for fibroblast growth factor 23 O-glycosylation by GalNAc-T3.

de Las Rivas, M.Paul Daniel, E.J.Narimatsu, Y.Companon, I.Kato, K.Hermosilla, P.Thureau, A.Ceballos-Laita, L.Coelho, H.Bernado, P.Marcelo, F.Hansen, L.Maeda, R.Lostao, A.Corzana, F.Clausen, H.Gerken, T.A.Hurtado-Guerrero, R.

(2020) Nat.Chem.Biol. --: --

  • DOI: 10.1038/s41589-019-0444-x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Polypeptide GalNAc-transferase T3 (GalNAc-T3) regulates fibroblast growth factor 23 (FGF23) by O-glycosylating Thr178 in a furin proprotein processing motif RHT <sup>178 </sup>R↓S. FGF23 regulates phosphate homeostasis and deficiency in GALNT3 or FGF ...

    Polypeptide GalNAc-transferase T3 (GalNAc-T3) regulates fibroblast growth factor 23 (FGF23) by O-glycosylating Thr178 in a furin proprotein processing motif RHT 178 R↓S. FGF23 regulates phosphate homeostasis and deficiency in GALNT3 or FGF23 results in hyperphosphatemia and familial tumoral calcinosis. We explored the molecular mechanism for GalNAc-T3 glycosylation of FGF23 using engineered cell models and biophysical studies including kinetics, molecular dynamics and X-ray crystallography of GalNAc-T3 complexed to glycopeptide substrates. GalNAc-T3 uses a lectin domain mediated mechanism to glycosylate Thr178 requiring previous glycosylation at Thr171. Notably, Thr178 is a poor substrate site with limiting glycosylation due to substrate clashes leading to destabilization of the catalytic domain flexible loop. We suggest GalNAc-T3 specificity for FGF23 and its ability to control circulating levels of intact FGF23 is achieved by FGF23 being a poor substrate. GalNAc-T3's structure further reveals the molecular bases for reported disease-causing mutations. Our findings provide an insight into how GalNAc-T isoenzymes achieve isoenzyme-specific nonredundant functions.


    Organizational Affiliation

    Department of Hematology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Laboratorio de Microscopías Avanzadas, Instituto de Nanociencia de Aragón, Universidad de Zaragoza, Zaragoza, Spain.,Swing Beamline, Synchrotron SOLEIL, Gif sur Yvette, France.,Fundación ARAID, Zaragoza, Spain.,Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, Copenhagen, Denmark.,Centre de Biochimie Structurale. INSERM, CNRS, Université de Montpellier, Montpellier, France.,Department of Eco-epidemiology, Institute of Tropical Medicine Nagasaki University, Nagasaki, Japan.,BIFI, University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain. rhurtado@bifi.es.,Department of Biochemistry, Case Western Reserve University, Cleveland, OH, USA.,Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, Logroño, Spain.,UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade de Nova de Lisboa, Caparica, Portugal.,Fundación ARAID, Zaragoza, Spain. rhurtado@bifi.es.,BIFI, University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain.,CIC bioGUNE, Bizkaia Technology Park, Derio, Spain.,Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza-CSIC, Zaragoza, Spain.,Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, Copenhagen, Denmark. rhurtado@bifi.es.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polypeptide N-acetylgalactosaminyltransferase
A
631Taeniopygia guttataMutation(s): 0 
Gene Names: GALNT3
EC: 2.4.1.-
Find proteins for H0ZAB5 (Taeniopygia guttata)
Go to Gene View: GALNT3
Go to UniProtKB:  H0ZAB5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ALA-THR-GLY-ALA-GLY-ALA-GLY-ALA-GLY-THR-THR-PRO-GLY-PRO
F
14N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, F
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
UDP
Query on UDP

Download SDF File 
Download CCD File 
A
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
TAM
Query on TAM

Download SDF File 
Download CCD File 
A
TRIS(HYDROXYETHYL)AMINOMETHANE
C7 H17 N O3
GKODZWOPPOTFGA-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
NGA
Query on NGA

Download SDF File 
Download CCD File 
F
N-ACETYL-D-GALACTOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-JAJWTYFOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.655α = 90.00
b = 104.661β = 90.00
c = 143.186γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2020-01-22
    Type: Database references