Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

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

Macromolecule Content

• Total Structure Weight: 47616.27 
• Atom Count: 3349 
• Residue Count: 399 
• Unique protein chains: 2

5L0R

human POGLUT1 in complex with Notch1 EGF12 and UDP

• DOI: 10.2210/pdb5L0R/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Homo sapiens


• Deposited: 2016-07-28 Released: 2017-08-09 
• Deposition Author(s): Li, Z., Rini, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.5 Å
• R-Value Free: 0.171 
• R-Value Work: 0.149 

Literature

Structural basis of Notch O-glucosylation and O-xylosylation by mammalian protein-O-glucosyltransferase 1 (POGLUT1).

Li, Z., Fischer, M., Satkunarajah, M., Zhou, D., Withers, S.G., Rini, J.M.

(2017) Nat Commun 8: 185-185

• PubMed: 28775322 
• DOI: 10.1038/s41467-017-00255-7
• Primary Citation of Related Structures:  
  5UB5, 5L0V, 5L0U, 5L0T, 5L0S


• PubMed Abstract: 
  

Protein O-glucosyltransferase 1/Rumi-mediated glucosylation of Notch epidermal growth factor-like (EGF-like) domains plays an important role in Notch signaling. Protein O-glucosyltransferase 1 shows specificity for folded EGF-like domains, it can only glycosylate serine residues in the C1XSXPC2 motif, and it possesses an uncommon dual donor substrate specificity. Using several EGF-like domains and donor substrate analogs, we have determined the structures of human Protein O-glucosyltransferase 1 substrate/product complexes that provide mechanistic insight into the basis for these properties. Notably, we show that Protein O-glucosyltransferase 1's requirement for folded EGF-like domains also leads to its serine specificity and that two distinct local conformational states are likely responsible for its ability to transfer both glucose and xylose. We also show that Protein O-glucosyltransferase 1 possesses the potential to xylosylate a much broader range of EGF-like domain substrates than was previously thought. Finally, we show that Protein O-glucosyltransferase 1 has co-evolved with EGF-like domains of the type found in Notch.POGLUT1 is a protein-O-glucosyltransferase that transfers glucose and xylose to the EGF-like domains of Notch and other signaling receptors. Here the authors report the structure of human POGLUT1 in complexes with 3 different EGF-like domains and donor substrates and shed light on the enzyme's substrate specificity and catalytic mechanism.

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Organizational Affiliation: 

Department of Biochemistry, University of Toronto, Toronto, ON, Canada, M5S 1A8.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Protein O-glucosyltransferase 1	A	357	Homo sapiens	Mutation(s): 0  Gene Names: POGLUT1 (C3orf9, CLP46, KTELC1, MDSRP) EC: 2.4.1.-
Find proteins for Q8NBL1 (Homo sapiens) Go to Gene View: POGLUT1 Go to UniProtKB:  Q8NBL1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Neurogenic locus notch homolog protein 1	B	42	Homo sapiens	Mutation(s): 0  Gene Names: NOTCH1 (TAN1)
Find proteins for P46531 (Homo sapiens) Go to Gene View: NOTCH1 Go to UniProtKB:  P46531

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
UDP	A	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.5 Å
• R-Value Free: 0.171 
• R-Value Work: 0.149 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 70.580	α = 90.00
b = 73.560	β = 90.00
c = 83.280	γ = 90.00

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-07-28 
• Released Date: 2017-08-09 
• Deposition Author(s): Li, Z., Rini, J.M.

Revision History 

• Version 1.0: 2017-08-09
  Type: Initial release
• Version 1.1: 2017-08-30
  Type: Database references