› 5lev

X-ray diffraction
3.2Å resolution

Crystal structure of human UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase (DPAGT1) (V264G mutant)

Released:
DOI: 10.2210/pdb5lev/pdb
PDB entry 5lev coloured by chain, front view.
PDB entry 5lev coloured by chain, side view.
PDB entry 5lev coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structures of DPAGT1 Explain Glycosylation Disease Mechanisms and Advance TB Antibiotic Design.
Dong YY, Wang H, Pike ACW, Cochrane SA, Hamedzadeh S, Wyszyński FJ, Bushell SR, Royer SF, Widdick DA, Sajid A, Boshoff HI, Park Y, Lucas R, Liu WM, Lee SS, Machida T, Minall L, Mehmood S, Belaya K, Liu WW, Chu A, Shrestha L, Mukhopadhyay SMM, Strain-Damerell C, Chalk R, Burgess-Brown NA, Bibb MJ, Barry Iii CE, Robinson CV, Beeson D, Davis BG, Carpenter EP
Cell 175 1045-1058.e16 (2018)
PMID: 30388443

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-190577 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase Chain: A
Molecule details ›
Chain: A
Length: 409 amino acids
Theoretical weight: 46.17 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

1 bound ligand:
Ligand UNL 1 x UNL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P6522
Unit cell:
a: 103.25Å b: 103.25Å c: 239.15Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.235 0.234 0.24
Expression system: Spodoptera frugiperda

Quick links

Citations

8 review citations

Natural products as modulators of eukaryotic protein secretion.
Luesch et al. (2020)
7 more

5 mentions without citation

Structure-Based Insight on the Mechanism of N-Glycosylation Inhibition by Tunicamycin.
Yoon et al. (2023)
4 more