1ON8

Crystal structure of mouse alpha-1,4-N-acetylhexosaminyltransferase (EXTL2) with UDP and GlcUAb(1-3)Galb(1-O)-naphthalenelmethanol an acceptor substrate analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 

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This is version 2.0 of the entry. See complete history


Literature

Crystal structure of an alpha-1,4-N-acetylhexosaminyltransferase (EXTL2), a member of the exostosin gene family involved in heparan sulfate biosynthesis

Pedersen, L.C.Dong, J.Taniguchi, F.Kitagawa, H.Krahn, J.M.Pedersen, L.G.Sugahara, K.Negishi, M.

(2003) J Biol Chem 278: 14420-14428

  • DOI: 10.1074/jbc.M210532200
  • Primary Citation of Related Structures:  
    1OMX, 1OMZ, 1ON6, 1ON8

  • PubMed Abstract: 
  • EXTL2, an alpha1,4-N-acetylhexosaminyltransferase, catalyzes the transfer reaction of N-acetylglucosamine and N-acetylgalactosamine from the respective UDP-sugars to the non-reducing end of [glucuronic acid]beta1-3[galactose]beta1-O-naphthalenemethanol, an acceptor substrate analog of the natural common linker of various glycosylaminoglycans ...

    EXTL2, an alpha1,4-N-acetylhexosaminyltransferase, catalyzes the transfer reaction of N-acetylglucosamine and N-acetylgalactosamine from the respective UDP-sugars to the non-reducing end of [glucuronic acid]beta1-3[galactose]beta1-O-naphthalenemethanol, an acceptor substrate analog of the natural common linker of various glycosylaminoglycans. We have solved the x-ray crystal structure of the catalytic domain of mouse EXTL2 in the apo-form and with donor substrates UDP-N-acetylglucosamine and UDP-N-acetylgalactosamine. In addition, a structure of the ternary complex with UDP and the acceptor substrate analog [glucuronic acid]beta1-3[galactose]beta1-O-naphthalenemethanol has been determined. These structures reveal three highly conserved residues, Asn-243, Asp-246, and Arg-293, located at the active site. Mutation of these residues greatly decreases the activity. In the ternary complex, an interaction exists between the beta-phosphate of the UDP leaving group and the acceptor hydroxyl of the substrate that may play a functional role in catalysis. These structures represent the first structures from the exostosin gene family and provide important insight into the mechanisms of alpha1,4-N-acetylhexosaminyl transfer in heparan biosynthesis.


    Organizational Affiliation

    Pharmacogenetics Section, Laboratory of Reproductive and Developmental Toxicology, National Institute of Environmental Health Sciences, National Institute of Health, Research Triangle Park, North Carolina 27709, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha-1,4-N-acetylhexosaminyltransferase EXTL2A, B293Mus musculusMutation(s): 0 
Gene Names: EXTL2 OR EXTR2Extl2Extr2
EC: 2.4.1 (PDB Primary Data), 2.4.1.223 (UniProt)
UniProt
Find proteins for Q9ES89 (Mus musculus)
Explore Q9ES89 
Go to UniProtKB:  Q9ES89
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ES89
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-glucopyranuronic acid-(1-3)-beta-D-galactopyranoseC, D 2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G99041PQ
GlyCosmos:  G99041PQ
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UDP
Query on UDP

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B]
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.157α = 90
b = 125.157β = 90
c = 83.692γ = 90
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-22
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary