7DXI | pdb_00007dxi

Structure of Drosophila melanogaster GlcNAc-1-phosphotransferase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structural insights into how GlcNAc-1-phosphotransferase directs lysosomal protein transport.

Du, S.Wang, G.Zhang, Z.Ma, C.Gao, N.Xiao, J.

(2022) J Biological Chem 298: 101702-101702

  • DOI: https://doi.org/10.1016/j.jbc.2022.101702
  • Primary Citation Related Structures: 
    7DXI

  • PubMed Abstract: 

    GlcNAc-1-phosphotransferase catalyzes the initial step in the formation of the mannose-6-phosphate tag that labels ∼60 lysosomal proteins for transport. Mutations in GlcNAc-1-phosphotransferase are known to cause lysosomal storage disorders such as mucolipidoses. However, the molecular mechanism of GlcNAc-1-phosphotransferase activity remains unclear. Mammalian GlcNAc-1-phosphotransferases are α2β2γ2 hexamers in which the core catalytic α- and β-subunits are derived from the GNPTAB (N-acetylglucosamine-1-phosphate transferase subunits alpha and beta) gene. Here, we present the cryo-electron microscopy structure of the Drosophila melanogaster GNPTAB homolog, DmGNPTAB. We identified four conserved regions located far apart in the sequence that fold into the catalytic domain, which exhibits structural similarity to that of the UDP-glucose glycoprotein glucosyltransferase. Comparison with UDP-glucose glycoprotein glucosyltransferase also revealed a putative donor substrate-binding site, and the functional requirements of critical residues in human GNPTAB were validated using GNPTAB-knockout cells. Finally, we show that DmGNPTAB forms a homodimer that is evolutionarily conserved and that perturbing the dimer interface undermines the maturation and activity of human GNPTAB. These results provide important insights into GlcNAc-1-phosphotransferase function and related diseases.


  • Organizational Affiliation
    • State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China; School of Life Sciences, Peking University, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 135.93 kDa 
  • Atom Count: 6,130 
  • Modeled Residue Count: 742 
  • Deposited Residue Count: 1,162 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
FI02838p
A, B
581Drosophila melanogasterMutation(s): 0 
Gene Names: Dmel\CG8027Cg8027CG8027-RADmel_CG8027
UniProt
Find proteins for A1Z7S7 (Drosophila melanogaster)
Explore A1Z7S7 
Go to UniProtKB:  A1Z7S7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1Z7S7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2022-08-17
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Structure summary
  • Version 1.3: 2025-06-25
    Changes: Data collection