› 2g9f

X-ray diffraction
1.9Å resolution

Crystal structure of intein-tagged mouse PNGase C-terminal domain

Released:
DOI: 10.2210/pdb2g9f/pdb
PDB entry 2g9f coloured by chain, front view.
PDB entry 2g9f coloured by chain, side view.
PDB entry 2g9f coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Structural and biochemical studies of the C-terminal domain of mouse peptide-N-glycanase identify it as a mannose-binding module.
Zhou X, Zhao G, Truglio JJ, Wang L, Li G, Lennarz WJ, Schindelin H
Proc Natl Acad Sci U S A 103 17214-9 (2006)
PMID: 17088551

Function and Biology Details

Reaction catalysed: 
Hydrolysis of an N(4)-(acetyl-beta-D-glucosaminyl)asparagine residue in which the glucosamine residue may be further glycosylated, to yield a (substituted) N-acetyl-beta-D-glucosaminylamine and a peptide containing an aspartate residue
Biochemical function:
  • not assigned
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-191601 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase Chain: A
Molecule details ›
Chain: A
Length: 201 amino acids
Theoretical weight: 22.96 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9JI78 (Residues: 451-651; Coverage: 31%)
Gene name: Ngly1
Sequence domains: PNGase C-terminal domain, mannose-binding module PAW
Structure domains: Peptide N glycanase, PAW domain

Ligands and Environments

2 bound ligands:
Ligand CL 1 x CL
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X26C
Spacegroup: P3221
Unit cell:
a: 40.76Å b: 40.76Å c: 193.663Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.169 0.167 0.213
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

8 review citations

The cytoplasmic peptide:N-glycanase (NGLY1) - Structure, expression and cellular functions.
Suzuki et al. (2016)
7 more

1 mention without citation

Structural and biochemical studies of the C-terminal domain of mouse peptide-N-glycanase identify it as a mannose-binding module.
Zhou et al. (2006)