› 2cbi

X-ray diffraction
2.25Å resolution

Structure of the Clostridium perfringens NagJ family 84 glycoside hydrolase, a homologue of human O-GlcNAcase

Released:
DOI: 10.2210/pdb2cbi/pdb
PDB entry 2cbi coloured by chain, front view.
PDB entry 2cbi coloured by chain, side view.
PDB entry 2cbi coloured by chain, top view.
Source organism: Clostridium perfringens
Primary publication:
Structural insights into the mechanism and inhibition of eukaryotic O-GlcNAc hydrolysis.
Rao FV, Dorfmueller HC, Villa F, Allwood M, Eggleston IM, van Aalten DM
EMBO J 25 1569-78 (2006)
PMID: 16541109

Function and Biology Details

Reaction catalysed: 
[Protein]-3-O-(N-acetyl-beta-D-glucosaminyl)-L-serine + H(2)O = [protein]-L-serine + N-acetyl-D-glucosamine
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-171162 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
O-GlcNAcase NagJ Chains: A, B
Molecule details ›
Chains: A, B
Length: 594 amino acids
Theoretical weight: 66.69 KDa
Source organism: Clostridium perfringens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q0TR53 (Residues: 31-624; Coverage: 61%)
Gene names: CPF_1442, nagJ
Sequence domains:
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand SO4 1 x SO4
Ligand CL 1 x CL
Ligand GBL 2 x GBL
Ligand GOL 2 x GOL
Ligand ZN 11 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM14
Spacegroup: I212121
Unit cell:
a: 119.939Å b: 147.38Å c: 157.687Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.169 0.169 0.22
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

30 review citations

Cross talk between O-GlcNAcylation and phosphorylation: roles in signaling, transcription, and chronic disease.
Hart et al. (2011)
29 more

3 mentions without citation

Structural insights into the mechanism and inhibition of eukaryotic O-GlcNAc hydrolysis.
Rao et al. (2006)
2 more