7VMT

Crystal structure of murine N-acetylglucosaminyl transferase IVa (GnT-IVa) lectin domain in unliganded form

  • Classification: SUGAR BINDING PROTEIN
  • Organism(s): Mus musculus
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2021-10-09 Released: 2022-06-15 
  • Deposition Author(s): Nagae, M.
  • Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Discovery of a lectin domain that regulates enzyme activity in mouse N-acetylglucosaminyltransferase-IVa (MGAT4A).

Nagae, M., Hirata, T., Tateno, H., Mishra, S.K., Manabe, N., Osada, N., Tokoro, Y., Yamaguchi, Y., Doerksen, R.J., Shimizu, T., Kizuka, Y.

(2022) Commun Biol 5: 695-695

  • DOI: https://doi.org/10.1038/s42003-022-03661-w
  • Primary Citation of Related Structures:  
    7VMT

  • PubMed Abstract: 

    • N-Glycosylation is a common post-translational modification, and the number of GlcNAc branches in N-glycans impacts glycoprotein functions. N-Acetylglucosaminyltransferase-IVa (GnT-IVa, also designated as MGAT4A) forms a β1-4 GlcNAc branch on the α1-3 mannose arm in N-glycans ...

    N-Glycosylation is a common post-translational modification, and the number of GlcNAc branches in N-glycans impacts glycoprotein functions. N-Acetylglucosaminyltransferase-IVa (GnT-IVa, also designated as MGAT4A) forms a β1-4 GlcNAc branch on the α1-3 mannose arm in N-glycans. Downregulation or loss of GnT-IVa causes diabetic phenotypes by dysregulating glucose transporter-2 in pancreatic β-cells. Despite the physiological importance of GnT-IVa, its structure and catalytic mechanism are poorly understood. Here, we identify the lectin domain in mouse GnT-IVa's C-terminal region. The crystal structure of the lectin domain shows structural similarity to a bacterial GlcNAc-binding lectin. Comprehensive glycan binding assay using 157 glycans and solution NMR reveal that the GnT-IVa lectin domain selectively interacts with the product N-glycans having a β1-4 GlcNAc branch. Point mutation of the residue critical to sugar recognition impairs the enzymatic activity, suggesting that the lectin domain is a regulatory subunit for efficient catalytic reaction. Our findings provide insights into how branching structures of N-glycans are biosynthesized.

    Organizational Affiliation: 

    Institute for Glyco-core Research (iGCORE), Gifu University, Gifu, Japan. kizuka@gifu-u.ac.jp.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase A soluble form
A, B, C, D, E, F
A, B, C, D, E, F
149Mus musculusMutation(s): 1 
Gene Names: Mgat4a
EC: 2.4.1.145
UniProt
Find proteins for Q812G0 (Mus musculus)
Explore Q812G0 
Go to UniProtKB:  Q812G0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ812G0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BTB
Query on BTB
Download Ideal Coordinates CCD File 
G [auth A],
H [auth B],
I [auth F]		2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.913α = 90
b = 82.499β = 105.659
c = 148.866γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
CRANK2phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2022-06-15 
    • Deposition Author(s): Nagae, M.
Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan20K06575

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-15
    Type: Initial release
  • Version 1.1: 2022-07-27
    Changes: Database references