7JHM

Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 with N-acetyl-lactosamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report



Literature

Structures and mechanism of human glycosyltransferase beta 1,3-N-acetylglucosaminyltransferase 2 (B3GNT2), an important player in immune homeostasis.

Hao, Y.Crequer-Grandhomme, A.Javier, N.Singh, A.Chen, H.Manzanillo, P.Lo, M.C.Huang, X.

(2020) J Biol Chem 

  • DOI: 10.1074/jbc.RA120.015306
  • Primary Citation of Related Structures:  
    7JHO, 7JHM, 7JHN, 7JHK, 7JHL, 7JHI

  • PubMed Abstract: 
  • β1,3- N -acetylglucosaminyltransferases (B3GNTs) are Golgi-resident glycosyltransferases involved in the biosynthesis of poly- N -acetyl-lactosamine chains. They catalyze the addition of the N -acetylglucosamine to the N -acetyl-lactosamine repeat as a key step of the chain elongation process ...

    β1,3- N -acetylglucosaminyltransferases (B3GNTs) are Golgi-resident glycosyltransferases involved in the biosynthesis of poly- N -acetyl-lactosamine chains. They catalyze the addition of the N -acetylglucosamine to the N -acetyl-lactosamine repeat as a key step of the chain elongation process. Poly- N -acetyl-lactosamine is involved in immune system in many ways. Particularly, its long chain has been demonstrated to suppress excessive immune responses. Among the characterized B3GNTs, B3GNT2 is the major poly- N -acetyl-lactosamine synthase and deletion of its coding gene dramatically reduced the cell surface poly- N -acetyl-lactosamine and led to hypersensitive and hyperresponsive immunocytes. Despite the extensive functional studies, no structural information is available to understand the molecular mechanism of B3GNT2, as well as other B3GNTs. Here we present the structural and kinetic studies of the human B3GNT2. Five crystal structures of B3GNT2 have been determined in the unliganded, donor substrate-bound, acceptor substrate-bound and product(s)-bound states at resolutions ranging from 1.85 Å to 2.35 Å. Kinetic study shows that the transglycosylation reaction follows a sequential mechanism. Critical residues involved in recognition of both donor and acceptor substrates as well as catalysis are identified. Mutations of these invariant residues impair B3GNT2 activity in cell assays. Structural comparison with other glycosyltransferases such as mouse Fringe reveals a novel N-terminal helical domain of B3GNTs that may stabilize the catalytic domain and distinguish among different acceptor substrates.


    Organizational Affiliation

    Amgen Research, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2AB370Homo sapiensMutation(s): 0 
Gene Names: B3GNT2B3GALT7B3GNT1
EC: 2.4.1.149
Find proteins for Q9NY97 (Homo sapiens)
Explore Q9NY97 
Go to UniProtKB:  Q9NY97
NIH Common Fund Data Resources
PHAROS  Q9NY97
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D
5 N-Glycosylation Oligosaccharides Interaction
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, G
2 N/A Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P6G
Query on P6G

Download CCD File 
A
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
A, B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.509α = 90
b = 76.992β = 105.06
c = 134.389γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2020-07-20 
  • Released Date: 2020-11-18 
  • Deposition Author(s): Hao, Y., Huang, X.

Revision History 

  • Version 1.0: 2020-11-18
    Type: Initial release