5NDF

Small-molecule inhibition of ppGalNAc-Ts selectively reduces mucin-type O-glycosylation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The small molecule luteolin inhibits N-acetyl-alpha-galactosaminyltransferases and reduces mucin-type O-glycosylation of amyloid precursor protein.

Liu, F.Xu, K.Xu, Z.de Las Rivas, M.Wang, C.Li, X.Lu, J.Zhou, Y.Delso, I.Merino, P.Hurtado-Guerrero, R.Zhang, Y.Wu, F.

(2017) J Biol Chem 292: 21304-21319

  • DOI: https://doi.org/10.1074/jbc.M117.814202
  • Primary Citation of Related Structures:  
    5NDF

  • PubMed Abstract: 

    Mucin-type O -glycosylation is the most abundant type of O -glycosylation. It is initiated by the members of the polypeptide N -acetyl-α-galactosaminyltransferase (ppGalNAc-T) family and closely associated with both physiological and pathological conditions, such as coronary artery disease or Alzheimer's disease. The lack of direct and selective inhibitors of ppGalNAc-Ts has largely impeded research progress in understanding the molecular events in mucin-type O -glycosylation. Here, we report that a small molecule, the plant flavonoid luteolin, selectively inhibits ppGalNAc-Ts in vitro and in cells. We found that luteolin inhibits ppGalNAc-T2 in a peptide/protein-competitive manner but not promiscuously ( e.g. via aggregation-based activity). X-ray structural analysis revealed that luteolin binds to the P X P motif-binding site found in most protein substrates, which was further validated by comparing the interactions of luteolin with wild-type enzyme and with mutants using 1 H NMR-based binding experiments. Functional studies disclosed that luteolin at least partially reduced production of β-amyloid protein by selectively inhibiting the activity of ppGalNAc-T isoforms. In conclusion, our study provides key structural and functional details on luteolin inhibiting ppGalNAc-T activity, opening up the way for further optimization of more potent and specific ppGalNAc-T inhibitors. Moreover, our findings may inform future investigations into site-specific O -GalNAc glycosylation and into the molecular mechanism of luteolin-mediated ppGalNAc-T inhibition.


  • Organizational Affiliation

    From the Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polypeptide N-acetylgalactosaminyltransferase 2
A, B, C, D, E
A, B, C, D, E, F
571Homo sapiensMutation(s): 1 
Gene Names: GALNT2
EC: 2.4.1.41
UniProt & NIH Common Fund Data Resources
Find proteins for Q10471 (Homo sapiens)
Explore Q10471 
Go to UniProtKB:  Q10471
PHAROS:  Q10471
GTEx:  ENSG00000143641 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ10471
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UDP
Query on UDP

Download Ideal Coordinates CCD File 
AA [auth E]
DA [auth F]
H [auth A]
P [auth B]
T [auth C]
AA [auth E],
DA [auth F],
H [auth A],
P [auth B],
T [auth C],
W [auth D]
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
LU2
Query on LU2

Download Ideal Coordinates CCD File 
N [auth A],
R [auth B],
Y [auth D]
2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one
C15 H10 O6
IQPNAANSBPBGFQ-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
BA [auth E]
EA [auth F]
I [auth A]
J [auth A]
K [auth A]
BA [auth E],
EA [auth F],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
Q [auth B],
U [auth C],
X [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
CA [auth F]
G [auth A]
O [auth B]
S [auth C]
V [auth D]
CA [auth F],
G [auth A],
O [auth B],
S [auth C],
V [auth D],
Z [auth E]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.98α = 90
b = 123.111β = 90
c = 248.152γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
MICINNSpainBFU2016-75633-P
MICINNSpainCTQ2013-44367-C2-2-P

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-01
    Type: Initial release
  • Version 1.1: 2018-01-10
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description