5NQA

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.226 

Starting Model: experimental
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This is version 1.3 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: https://doi.org/10.1038/s41467-017-02006-0
  • Primary Citation of Related Structures:  
    5NQA

  • 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-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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polypeptide N-acetylgalactosaminyltransferase 4
A, B
578Homo sapiensMutation(s): 0 
Gene Names: GALNT4
EC: 2.4.1.41
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N4A0 (Homo sapiens)
Explore Q8N4A0 
Go to UniProtKB:  Q8N4A0
PHAROS:  Q8N4A0
GTEx:  ENSG00000257594 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N4A0
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Monoglycopeptide 3C [auth G]16Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NGA
Query on NGA
Download Ideal Coordinates CCD File 
HC [auth G],
UA [auth A]		2-acetamido-2-deoxy-beta-D-galactopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-JAJWTYFOSA-N
GOL
Query on GOL
Download Ideal Coordinates CCD File 
DC [auth B]
EC [auth B]
FC [auth B]
GC [auth B]
OA [auth A]
DC [auth B],
EC [auth B],
FC [auth B],
GC [auth B],
OA [auth A],
PA [auth A],
QA [auth A],
RA [auth A],
SA [auth A],
TA [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO
Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth B]
AC [auth B]
BA [auth A]
BB [auth B]
AA [auth A],
AB [auth B],
AC [auth B],
BA [auth A],
BB [auth B],
BC [auth B],
CA [auth A],
CB [auth B],
CC [auth B],
D [auth A],
DA [auth A],
DB [auth B],
E [auth A],
EA [auth A],
EB [auth B],
F [auth A],
FA [auth A],
FB [auth B],
G [auth A],
GA [auth A],
GB [auth B],
H [auth A],
HA [auth A],
HB [auth B],
I [auth A],
IA [auth A],
IB [auth B],
J [auth A],
JA [auth A],
JB [auth B],
K [auth A],
KA [auth A],
KB [auth B],
L [auth A],
LA [auth A],
LB [auth B],
M [auth A],
MA [auth A],
MB [auth B],
N [auth A],
NA [auth A],
NB [auth B],
O [auth A],
OB [auth B],
P [auth A],
PB [auth B],
Q [auth A],
QB [auth B],
R [auth A],
RB [auth B],
S [auth A],
SB [auth B],
T [auth A],
TB [auth B],
U [auth A],
UB [auth B],
V [auth A],
VA [auth B],
VB [auth B],
W [auth A],
WA [auth B],
WB [auth B],
X [auth A],
XA [auth B],
XB [auth B],
Y [auth A],
YA [auth B],
YB [auth B],
Z [auth A],
ZA [auth B],
ZB [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.226 
  • 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
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.3: 2024-10-16
    Changes: Structure summary