Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.82 kDa 
• Atom Count: 2901 
• Modelled Residue Count: 349 
• Deposited Residue Count: 383 
• Unique protein chains: 1

4UZ5

STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM IV - 2.1A

• DOI: 10.2210/pdb4UZ5/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2014-09-04 Released: 2015-02-25 
• Deposition Author(s): Zebisch, M., Jones, E.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.237 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

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

• PubMed: 25731175 
• DOI: 10.1038/nature14259
• Primary Citation of Related Structures:  
  4UZ1, 4UZ5, 4UYU, 4UZ6, 4UZ7, 4UYW, 4UZQ, 4UZJ, 4UZK, 4UZL


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NOTUM	A	383	Homo sapiens	Mutation(s): 1  Gene Names: NOTUM, OK/SW-CL.30 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.237 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.416	α = 90
b = 138.416	β = 90
c = 138.416	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-09-04 
• Released Date: 2015-02-25 
Deposition Author(s): Zebisch, M., Jones, E.Y.

Revision History  

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