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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1038/nature14259
  • Structures With Same Primary Citation

  • 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 ac ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN NOTUM HOMOLOG
A
386Homo sapiensMutation(s): 2 
Gene Names: NOTUMOK/SW-CL.30
EC: 3.1.1.1 (PDB Primary Data), 3.1.1.98 (UniProt)
Find proteins for Q6P988 (Homo sapiens)
Go to UniProtKB:  Q6P988
NIH Common Fund Data Resources
PHAROS  Q6P988
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN WNT-7A
B
8Homo sapiensMutation(s): 0 
Gene Names: WNT7A
Find proteins for O00755 (Homo sapiens)
Go to UniProtKB:  O00755
NIH Common Fund Data Resources
PHAROS  O00755
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAM
Query on PAM

Download CCD File 
B
PALMITOLEIC ACID
C16 H30 O2
SECPZKHBENQXJG-FPLPWBNLSA-N
 Ligand Interaction
NAG
Query on NAG

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

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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