4WLG

crystal structure of mouse Xyloside xylosyltransferase 1, apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Xyloside xylosyltransferase 1
A, B
306Mus musculusMutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3U4G3
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.804α = 90
b = 88.804β = 90
c = 154.324γ = 120
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2015-11-04 
  • Deposition Author(s): Yu, H., Li, H.

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-04
    Type: Initial release
  • Version 1.1: 2016-04-20
    Changes: Database references
  • Version 1.2: 2023-12-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2024-10-30
    Changes: Structure summary