5NQA

Crystal structure of GalNAc-T4 in complex with the monoglycopeptide 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The interdomain flexible linker of the polypeptide GalNAc transferases dictates their long-range glycosylation preferences.

Rivas, M.L.Lira-Navarrete, E.Daniel, E.J.P.Companon, I.Coelho, H.Diniz, A.Jimenez-Barbero, J.Peregrina, J.M.Clausen, H.Corzana, F.Marcelo, F.Jimenez-Oses, G.Gerken, T.A.Hurtado-Guerrero, R.

(2017) Nat Commun 8: 1959-1959

  • DOI: 10.1038/s41467-017-02006-0

  • PubMed Abstract: 
  • The polypeptide GalNAc-transferases (GalNAc-Ts), that initiate mucin-type O-glycosylation, consist of a catalytic and a lectin domain connected by a flexible linker. In addition to recognizing polypeptide sequence, the GalNAc-Ts exhibit unique long-r ...

    The polypeptide GalNAc-transferases (GalNAc-Ts), that initiate mucin-type O-glycosylation, consist of a catalytic and a lectin domain connected by a flexible linker. In addition to recognizing polypeptide sequence, the GalNAc-Ts exhibit unique long-range N- and/or C-terminal prior glycosylation (GalNAc-O-Ser/Thr) preferences modulated by the lectin domain. Here we report studies on GalNAc-T4 that reveal the origins of its unique N-terminal long-range glycopeptide specificity, which is the opposite of GalNAc-T2. The GalNAc-T4 structure bound to a monoglycopeptide shows that the GalNAc-binding site of its lectin domain is rotated relative to the homologous GalNAc-T2 structure, explaining their different long-range preferences. Kinetics and molecular dynamics simulations on several GalNAc-T2 flexible linker constructs show altered remote prior glycosylation preferences, confirming that the flexible linker dictates the rotation of the lectin domain, thus modulating the GalNAc-Ts' long-range preferences. This work for the first time provides the structural basis for the different remote prior glycosylation preferences of the GalNAc-Ts.


    Organizational Affiliation

    BIFI, University of Zaragoza, BIFI-IQFR (CSIC) Joint Unit, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, 50018, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polypeptide N-acetylgalactosaminyltransferase 4
A, B
578Homo sapiensMutation(s): 0 
Gene Names: GALNT4
EC: 2.4.1.41
Find proteins for Q8N4A0 (Homo sapiens)
Go to Gene View: GALNT4
Go to UniProtKB:  Q8N4A0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Monoglycopeptide 3
G
16N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NGA
Query on NGA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.225 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 65.447α = 116.47
b = 79.881β = 96.74
c = 88.614γ = 104.72
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2017-12-20
    Type: Initial release