Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 42.04 kDa 
• Atom Count: 2905 
• Modelled Residue Count: 334 
• Deposited Residue Count: 356 
• Unique protein chains: 2

4WMA

Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese,acceptor ligand and UDP-Glucose

• PDB DOI: 10.2210/pdb4WMA/pdb

• Classification: transferase/protein binding
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): No 


• Deposited: 2014-10-08 Released: 2015-09-30 
• Deposition Author(s): Yu, H., Li, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.243 
• R-Value Work: 0.219 
• R-Value Observed: 0.220 

Literature

Notch-modifying xylosyltransferase structures support an SNi-like retaining mechanism.

Yu, H., Takeuchi, M., LeBarron, J., Kantharia, J., London, E., Bakker, H., Haltiwanger, R.S., Li, H., Takeuchi, H.

(2015) Nat Chem Biol 11: 847-854

• PubMed: 26414444 
• DOI: 10.1038/nchembio.1927
• Primary Citation of Related Structures:  
  4WLG, 4WLM, 4WLZ, 4WM0, 4WMA, 4WMB, 4WMI, 4WMK, 4WN2


• PubMed Abstract: 
  

A major question remaining in glycobiology is how a glycosyltransferase (GT) that retains the anomeric linkage of a sugar catalyzes the reaction. Xyloside α-1,3-xylosyltransferase (XXYLT1) is a retaining GT that regulates Notch receptor activation by adding xylose to the Notch extracellular domain. Here, using natural acceptor and donor substrates and active Mus musculus XXYLT1, we report a series of crystallographic snapshots along the reaction, including an unprecedented natural and competent Michaelis reaction complex for retaining enzymes. These structures strongly support the SNi-like reaction as the retaining mechanism for XXYLT1. Unexpectedly, the epidermal growth factor-like repeat acceptor substrate undergoes a large conformational change upon binding to the active site, providing a structural basis for substrate specificity. Our improved understanding of this retaining enzyme will accelerate the design of retaining GT inhibitors that can modulate Notch activity in pathological situations in which Notch dysregulation is known to cause cancer or developmental disorders.

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Organizational Affiliation: 

Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xyloside xylosyltransferase 1	A	306	Mus musculus	Mutation(s): 0  Gene Names: Xxylt1 EC: 2.4.2 (PDB Primary Data), 2.4.2.62 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q3U4G3 (Mus musculus) Explore Q3U4G3  Go to UniProtKB:  Q3U4G3
IMPC:  MGI:2146443

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor IX	B [auth D]	50	Homo sapiens	Mutation(s): 0  Gene Names: F9 EC: 3.4.21.22
UniProt & NIH Common Fund Data Resources
Find proteins for P00740 (Homo sapiens) Explore P00740  Go to UniProtKB:  P00740
PHAROS:  P00740

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-xylopyranose-(1-3)-beta-D-glucopyranose	C [auth B]	2		O-Glycosylation
Glycosylation Resources
GlyTouCan:  G01629YL GlyCosmos:  G01629YL GlyGen:  G01629YL

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UPG	E [auth A]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C15 H24 N2 O17 P2 HSCJRCZFDFQWRP-JZMIEXBBSA-N
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MN	D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.243 
• R-Value Work: 0.219 
• R-Value Observed: 0.220 
• Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.028	α = 90
b = 90.028	β = 90
c = 43.136	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-10-08 
• Released Date: 2015-09-30 
Deposition Author(s): Yu, H., Li, H.

Revision History  

• Version 1.0: 2015-09-30
  Type: Initial release
  
• Version 1.1: 2016-04-20
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary