› 6ibo

X-ray diffraction
2.17Å resolution

Catalytic deficiency of O-GlcNAc transferase leads to X-linked intellectual disability

Released:
DOI: 10.2210/pdb6ibo/pdb
PDB entry 6ibo coloured by chain, front view.
PDB entry 6ibo coloured by chain, side view.
PDB entry 6ibo coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Catalytic deficiency of O-GlcNAc transferase leads to X-linked intellectual disability.
Pravata VM, Muha V, Gundogdu M, Ferenbach AT, Kakade PS, Vandadi V, Wilmes AC, Borodkin VS, Joss S, Stavridis MP, van Aalten DMF
Proc Natl Acad Sci U S A 116 14961-14970 (2019)
PMID: 31296563

Function and Biology Details

Reaction catalysed: 
UDP-N-acetyl-alpha-D-glucosamine + [protein]-L-serine = UDP + [protein]-3-O-(N-acetyl-beta-D-glucosaminyl)-L-serine
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127416 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit Chain: A
Molecule details ›
Chain: A
Length: 723 amino acids
Theoretical weight: 80.99 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O15294 (Residues: 323-1041; Coverage: 69%)
Gene name: OGT
Sequence domains:
ALA-VAL-SER-ARG-ALA Chain: C
Molecule details ›
Chain: C
Length: 9 amino acids
Theoretical weight: 932 Da
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand 12V 1 x 12V
Ligand PO4 2 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: F222
Unit cell:
a: 137.737Å b: 150.617Å c: 199.996Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.201 0.254
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

7 review citations

Role of O-Linked N-Acetylglucosamine Protein Modification in Cellular (Patho)Physiology.
Chatham et al. (2021)
6 more

1 mention without citation

Catalytic deficiency of O-GlcNAc transferase leads to X-linked intellectual disability.
Pravata et al. (2019)