› 7s6n

X-ray diffraction
2.7Å resolution

N-acetylglucosamine-1-phosphotransferase (GNPT) alpha and beta subunits (GNPTAB) catalytic domain, from zebrafish

Released:
DOI: 10.2210/pdb7s6n/pdb
PDB entry 7s6n coloured by chain, front view.
PDB entry 7s6n coloured by chain, side view.
PDB entry 7s6n coloured by chain, top view.
Source organisms:
Primary publication:
Structures of the mannose-6-phosphate pathway enzyme, GlcNAc-1-phosphotransferase.
Gorelik A, Illes K, Bui KH, Nagar B
Proc Natl Acad Sci U S A 119 e2203518119 (2022)
PMID: 35939698

Function and Biology Details

Reaction catalysed: 
UDP-N-acetyl-D-glucosamine + lysosomal-enzyme D-mannose = UMP + lysosomal-enzyme N-acetyl-D-glucosaminyl-phospho-D-mannose
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176251 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (5 distinct):
LNR domain-containing protein; N-acetylglucosamine-1-phosphotransferase subunit beta Chains: A, B
Molecule details ›
Chains: A, B
Length: 495 amino acids
Theoretical weight: 58.36 KDa
Source organisms: Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q54MP1 (Residues: 61-86, 87-258; Coverage: 16%)
  • Canonical: Q5RGJ8 (Residues: 894-1173; Coverage: 23%)
Gene names: DDB_G0285815, gnpta, gnptab, gpt1, si:ch211-234f20.3, zgc:122985
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Ligand NAG 2 x NAG
Ligand BMA 1 x BMA
Ligand MAN 1 x MAN
Carbohydrate polymer : NEW Components: NAG, FUC
Ligand NAG 1 x NAG
Ligand FUC 1 x FUC
Carbohydrate polymer : NEW Components: NAG, BMA
Ligand NAG 2 x NAG
Ligand BMA 1 x BMA
Carbohydrate polymer : NEW Components: NAG, FUC
Ligand NAG 2 x NAG
Ligand FUC 1 x FUC
2 bound ligands:
Ligand NAG 5 x NAG
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08B1-1
Spacegroup: P21
Unit cell:
a: 97.182Å b: 86.605Å c: 106.985Å
α: 90° β: 112.169° γ: 90°
R-values:
R R work R free
0.186 0.184 0.231
Expression system: Spodoptera frugiperda

Quick links

Citations

1 review citation

The host mannose-6-phosphate pathway and viral infection.
Liu et al. (2024)
1 other article