› 6bw6

X-ray diffraction
2.95Å resolution

Human GPT (DPAGT1) H129 variant in complex with tunicamycin

Released:
DOI: 10.2210/pdb6bw6/pdb
PDB entry 6bw6 coloured by chain, front view.
PDB entry 6bw6 coloured by chain, side view.
PDB entry 6bw6 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
GlcNAc-1-P-transferase-tunicamycin complex structure reveals basis for inhibition of N-glycosylation.
Yoo J, Mashalidis EH, Kuk ACY, Yamamoto K, Kaeser B, Ichikawa S, Lee SY
Nat Struct Mol Biol 25 217-224 (2018)
PMID: 29459785

Function and Biology Details

Reaction catalysed: 
UDP-N-acetyl-D-glucosamine + dolichyl phosphate = UMP + N-acetyl-D-glucosaminyl-diphosphodolichol
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-190578 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 417 amino acids
Theoretical weight: 47.2 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9H3H5 (Residues: 1-408; Coverage: 100%)
Gene names: DPAGT1, DPAGT2
Sequence domains:

Ligands and Environments

2 bound ligands:
Ligand TUM 4 x TUM
Ligand PGW 4 x PGW
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: C2
Unit cell:
a: 210.615Å b: 105.363Å c: 148.08Å
α: 90° β: 103.49° γ: 90°
R-values:
R R work R free
0.261 0.26 0.291
Expression system: Spodoptera frugiperda

Quick links

Citations

12 review citations

The Crosstalk of Endoplasmic Reticulum (ER) Stress Pathways with NF-κB: Complex Mechanisms Relevant for Cancer, Inflammation and Infection.
Schmitz et al. (2018)
11 more

8 mentions without citation

The surprising structural and mechanistic dichotomy of membrane-associated phosphoglycosyl transferases.
O'Toole et al. (2021)
7 more