skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Notch-modifying xylosyltransferase structures support an SNi-like retaining mechanism

Journal Article · · Nature Chemical Biology
 [1];  [2];  [3];  [3];  [3];  [3];  [4];  [3];  [3]
  1. Brookhaven National Lab. (BNL), Upton, NY (United States)
  2. Brookhaven National Lab. (BNL), Upton, NY (United States); Stony Brook Univ., Stony Brook, NY (United States)
  3. Stony Brook Univ., Stony Brook, NY (United States)
  4. Hannover Medical School, Hannover (Germany)
+ Show Author Affiliations

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. As a result, 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.

Research Organization:
Brookhaven National Laboratory (BNL), Upton, NY (United States)
Sponsoring Organization:
National Institute of Health
Grant/Contract Number:
SC00112704
OSTI ID:
1234375
Report Number(s):
BNL-111663-2015-JA
Journal Information:
Nature Chemical Biology, Vol. 11, Issue 11; ISSN 1552-4450
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 48 works
Citation information provided by
Web of Science

References (44)

Overview of the CCP 4 suite and current developments journal March 2011
Mechanistic evidence for a front-side, SNi-type reaction in a retaining glycosyltransferase journal August 2011
Exome Sequencing of Head and Neck Squamous Cell Carcinoma Reveals Inactivating Mutations in NOTCH1 journal July 2011
Rumi Is a CAP10 Domain Glycosyltransferase that Modifies Notch and Is Required for Notch Signaling journal January 2008
Relaxation Dynamics of Tryptophan in Water: A UV Fluorescence Up-Conversion and Molecular Dynamics Study journal September 2010
Identification of Glycosyltransferase 8 Family Members as Xylosyltransferases Acting on O -Glucosylated Notch Epidermal Growth Factor Repeats journal November 2009
Retaining Glycosyltransferase Mechanism Studied by QM/MM Methods: Lipopolysaccharyl-α-1,4-galactosyltransferase C Transfers α-Galactose via an Oxocarbenium Ion-like Transition State journal March 2012
A novel tumour-suppressor function for the Notch pathway in myeloid leukaemia journal May 2011
Molecular Cloning of a Xylosyltransferase That Transfers the Second Xylose to O -Glucosylated Epidermal Growth Factor Repeats of Notch journal November 2011
Developing inhibitors of glycan processing enzymes as tools for enabling glycobiology journal July 2012
Recent structures, evolution and mechanisms of glycosyltransferases journal October 2012
Loss-of-function mutations in Notch receptors in cutaneous and lung squamous cell carcinoma journal October 2011
Conformational plasticity of glycogenin and its maltosaccharide substrate during glycogen biogenesis journal December 2011
Rumi functions as both a protein O-glucosyltransferase and a protein O-xylosyltransferase journal September 2011
Substrate-Guided Front-Face Reaction Revealed by Combined Structural Snapshots and Metadynamics for the Polypeptide N -Acetylgalactosaminyltransferase 2 journal June 2014
UCSF Chimera?A visualization system for exploratory research and analysis journal January 2004
Regulation of mammalian Notch signaling and embryonic development by the protein O-glucosyltransferase Rumi journal April 2011
Detection of UDP-D-Xylose: -D-Xyloside  ->3Xylosyltransferase Activity in Human Hepatoma Cell Line HepG2 journal November 1996
Mechanistic Insight into Enzymatic Glycosyl Transfer with Retention of Configuration through Analysis of Glycomimetic Inhibitors journal January 2010
Recent structural and mechanistic insights into post-translational enzymatic glycosylation journal December 2012
Mechanisms of Tryptophan Fluorescence Shifts in Proteins journal May 2001
Incorporation of Prior Phase Information Strengthens Maximum-Likelihood Structure Refinement journal November 1998
Intermediate Trapping on a Mutant Retaining α-Galactosyltransferase Identifies an Unexpected Aspartate Residue journal April 2004
The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1. journal May 2012
Site-specific O -Glucosylation of the Epidermal Growth Factor-like (EGF) Repeats of Notch : EFFICIENCY OF GLYCOSYLATION IS AFFECTED BY PROPER FOLDING AND AMINO ACID SEQUENCE OF INDIVIDUAL EGF REPEATS journal August 2012
The carbohydrate-active enzymes database (CAZy) in 2013 journal November 2013
A conserved face of the Jagged/Serrate DSL domain is involved in Notch trans-activation and cis-inhibition journal July 2008
The Molecular Mechanism of Enzymatic Glycosyl Transfer with Retention of Configuration: Evidence for a Short-Lived Oxocarbenium-Like Species journal September 2011
Features and development of Coot journal March 2010
Synthesis and conformational characterization of the epidermal growth factor-like domain of blood coagulation factor IX carrying xylosyl-glucose journal January 2004
PHENIX: a comprehensive Python-based system for macromolecular structure solution journal January 2010
Evolution of distinct EGF domains with specific functions journal April 2005
Activity of the yeast MNN1  -1,3-mannosyltransferase requires a motif conserved in many other families of glycosyltransferases journal July 1998
Glycosyltransferases: Structures, Functions, and Mechanisms journal June 2008
Molecular replacement with MOLREP journal December 2009
From Fly Wings to Targeted Cancer Therapies: A Centennial for Notch Signaling journal March 2014
Geometric Attributes of Retaining Glycosyltransferase Enzymes Favor an Orthogonal Mechanism journal August 2013
Fringe-mediated extension of O-linked fucose in the ligand-binding region of Notch1 increases binding to mammalian Notch ligands journal May 2014
Significance of glycosylation in Notch signaling journal October 2014
The structure of a Ca2+-binding epidermal growth factor-like domain: Its role in protein-protein interactions journal July 1995
[20] Processing of X-ray diffraction data collected in oscillation mode book January 1997
Negative Regulation of Notch Signaling by Xylose journal June 2013
The Canonical Notch Signaling Pathway: Unfolding the Activation Mechanism journal April 2009
Human factor IX has a tetrasaccharide O-glycosidically linked to serine 61 through the fucose residue. journal September 1992

Cited By (10)

Emerging structural insights into glycosyltransferase-mediated synthesis of glycans journal August 2019
Structural Divergence in O-GlcNAc Glycans Displayed on Epidermal Growth Factor-like Repeats of Mammalian Notch1 journal July 2018
Critical Review of Plant Cell Wall Matrix Polysaccharide Glycosyltransferase Activities Verified by Heterologous Protein Expression journal July 2019
Structural basis of protein arginine rhamnosylation by glycosyltransferase EarP journal February 2018
Genome-wide linkage analysis in Spanish melanoma-prone families identifies a new familial melanoma susceptibility locus at 11q journal April 2018
Effects of Notch glycosylation on health and diseases journal December 2019
Probing the contribution of individual polypeptide GalNAc-transferase isoforms to the O -glycoproteome by inducible expression in isogenic cell lines journal October 2018
Structural analysis of Notch-regulating Rumi reveals basis for pathogenic mutations journal July 2016
Defining the enzymatic pathway for polymorphic O -glycosylation of the pneumococcal serine-rich repeat protein PsrP journal February 2017
Regulation of Notch Function by O-Glycosylation book January 2018

Similar Records

Structure of xyloglucan xylosyltransferase 1 reveals simple steric rules that define biological patterns of xyloglucan polymers
Journal Article · Mon May 21 00:00:00 EDT 2018 · Proceedings of the National Academy of Sciences of the United States of America · OSTI ID:1234375
+2 more
Regulation of chondroitin sulfate synthesis: effect of. beta. -xylosides on synthesis of chondroitin sulfate proteoglycan, chondroitin sulfate chains, and core protein
Journal Article · Sun Sep 25 00:00:00 EDT 1977 · J. Biol. Chem.; (United States) · OSTI ID:1234375
Catalytic versatility of Bacillus pumilus. beta. -xylosidase: glycosyl transfer and hydrolysis promoted with. cap alpha. - and. beta. -D-xylosyl fluoride
Journal Article · Tue Jun 02 00:00:00 EDT 1987 · Biochemistry; (United States) · OSTI ID:1234375
+3 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
cancer
carbohydrates
enzyme mechanisms
X-ray crystallography