4WN2

Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese, product ligand and UDP (Product complex III)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1038/nchembio.1927
  • Primary Citation of Related Structures:  

  • 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 ...

    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.


    Organizational Affiliation

    Biosciences Department, Brookhaven National Laboratory, Upton, New York, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Xyloside xylosyltransferase 1
A
306Mus musculusMutation(s): 0 
Gene Names: Xxylt1
EC: 2.4.2.n3
Find proteins for Q3U4G3 (Mus musculus)
Go to UniProtKB:  Q3U4G3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor IX
D
50Homo sapiensMutation(s): 0 
Gene Names: F9
EC: 3.4.21.22
Find proteins for P00740 (Homo sapiens)
Go to Gene View: F9
Go to UniProtKB:  P00740
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
GXX
Query on GXX

Download SDF File 
Download CCD File 
D
alpha-D-xylopyranosyl-(1->3)-alpha-D-xylopyranosyl-(1->3)-beta-D-glucopyranose
C16 H28 O14
BLASHPVRFCCALK-IVCVOHDKSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
UDP
Query on UDP

Download SDF File 
Download CCD File 
A
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.195 
  • Space Group: P 3
Unit Cell:
Length (Å)Angle (°)
a = 89.509α = 90.00
b = 89.509β = 90.00
c = 43.053γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-10-10 
  • 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
    Type: Database references