7XTM

Crystal structure of the C-terminal domain of Bombyx mori N-acetylglucosaminyltransferase IV


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.224 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure and sugar-binding ability of the C-terminal domain of N-acetylglucosaminyltransferase IV establish a new carbohydrate-binding module family.

Oka, N.Mori, S.Ikegaya, M.Park, E.Y.Miyazaki, T.

(2022) Glycobiology 32: 1153-1163

  • DOI: https://doi.org/10.1093/glycob/cwac058
  • Primary Citation of Related Structures:  
    7XTL, 7XTM, 7XTN

  • PubMed Abstract: 

    N-glycans are modified by glycosyltransferases in the endoplasmic reticulum and Golgi apparatus. N-acetylglucosaminyltransferase IV (GnT-IV) is a Golgi-localized glycosyltransferase that synthesizes complex-type N-glycans in vertebrates. This enzyme attaches N-acetylglucosamine (GlcNAc) to the α-1,3-linked mannose branch of the N-glycan core structure via a β-1,4 linkage. Deficiency of this enzyme is known to cause abnormal cellular functions, making it a vital enzyme for living organisms. However, there has been no report on its 3-dimensional structure to date. Here, we demonstrated that the C-terminal regions (named CBML) of human GnT-IVa and Bombyx mori ortholog have the ability to bind β-N-acetylglucosamine. In addition, we determined the crystal structures of human CBML, B. mori CBML, and its complex with β-GlcNAc at 1.97, 1.47, and 1.15 Å resolutions, respectively, and showed that they adopt a β-sandwich fold, similar to carbohydrate-binding module family 32 (CBM32) proteins. The regions homologous to CBML (≥24% identity) were found in GnT-IV isozymes, GnT-IVb, and GnT-IVc (known as GnT-VI), and the structure of B. mori CBML in complex with β-GlcNAc indicated that the GlcNAc-binding residues were highly conserved among these isozymes. These residues are also conserved with the GlcNAc-binding CBM32 domain of β-N-acetylhexosaminidase NagH from Clostridium perfringens despite the low sequence identity (<20%). Taken together with the phylogenetic analysis, these findings indicate that these CBMLs may be novel CBM family proteins with GlcNAc-binding ability.


  • Organizational Affiliation

    Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-acetylglucosaminyltransferase IV
A, B
164Bombyx moriMutation(s): 0 
Gene Names: MGAT4
UniProt
Find proteins for A0A6J2K041 (Bombyx mandarina)
Explore A0A6J2K041 
Go to UniProtKB:  A0A6J2K041
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6J2K041
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.733α = 90
b = 64.466β = 95.092
c = 78.81γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan19K15748

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-28
    Type: Initial release
  • Version 1.1: 2022-11-30
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2022-12-07
    Changes: Database references
  • Version 1.3: 2024-04-03
    Changes: Data collection, Refinement description