4UZQ

STRUCTURE OF THE WNT DEACYLASE NOTUM IN COMPLEX WITH O-PALMITOLEOYL SERINE - CRYSTAL FORM IX - 1.5A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.129 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Notum Deacylates Wnt Proteins to Suppress Signalling Activity.

Kakugawa, S.Langton, P.F.Zebisch, M.Howell, S.A.Chang, T.Liu, Y.Feizi, T.Bineva, G.O'Reilly, N.Snijders, A.P.Jones, E.Y.Vincent, J.

(2015) Nature 519: 187

  • DOI: https://doi.org/10.1038/nature14259
  • Primary Citation of Related Structures:  
    4UYU, 4UYW, 4UYZ, 4UZ1, 4UZ5, 4UZ6, 4UZ7, 4UZ9, 4UZA, 4UZJ, 4UZK, 4UZL, 4UZQ, 4WBH

  • PubMed Abstract: 

    Signalling by Wnt proteins is finely balanced to ensure normal development and tissue homeostasis while avoiding diseases such as cancer. This is achieved in part by Notum, a highly conserved secreted feedback antagonist. Notum has been thought to act as a phospholipase, shedding glypicans and associated Wnt proteins from the cell surface. However, this view fails to explain specificity, as glypicans bind many extracellular ligands. Here we provide genetic evidence in Drosophila that Notum requires glypicans to suppress Wnt signalling, but does not cleave their glycophosphatidylinositol anchor. Structural analyses reveal glycosaminoglycan binding sites on Notum, which probably help Notum to co-localize with Wnt proteins. They also identify, at the active site of human and Drosophila Notum, a large hydrophobic pocket that accommodates palmitoleate. Kinetic and mass spectrometric analyses of human proteins show that Notum is a carboxylesterase that removes an essential palmitoleate moiety from Wnt proteins and thus constitutes the first known extracellular protein deacylase.


  • Organizational Affiliation

    MRC's National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN NOTUM HOMOLOG386Homo sapiensMutation(s): 2 
EC: 3.1.1.1 (PDB Primary Data), 3.1.1.98 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P988 (Homo sapiens)
Explore Q6P988 
Go to UniProtKB:  Q6P988
PHAROS:  Q6P988
GTEx:  ENSG00000185269 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6P988
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q6P988-1
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN WNT-7A8Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O00755 (Homo sapiens)
Explore O00755 
Go to UniProtKB:  O00755
PHAROS:  O00755
GTEx:  ENSG00000154764 
Entity Groups  
UniProt GroupO00755
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PAM
Query on PAM

Download Ideal Coordinates CCD File 
I [auth B]PALMITOLEIC ACID
C16 H30 O2
SECPZKHBENQXJG-FPLPWBNLSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.129 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.513α = 90
b = 69.35β = 92.28
c = 120.967γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-25
    Type: Initial release
  • Version 1.1: 2015-03-04
    Changes: Structure summary
  • Version 1.2: 2015-03-18
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.4: 2024-11-13
    Changes: Data collection, Database references, Structure summary