› 2i74

X-ray diffraction
1.75Å resolution

Crystal structure of mouse Peptide N-Glycanase C-terminal domain in complex with mannopentaose

Released:
DOI: 10.2210/pdb2i74/pdb
PDB entry 2i74 coloured by chain, front view.
PDB entry 2i74 coloured by chain, side view.
PDB entry 2i74 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
Macromolecules (2 distinct):
Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase Chains: A, B
Molecule details ›
Chains: A, B
Length: 189 amino acids
Theoretical weight: 21.99 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9JI78 (Residues: 471-651; Coverage: 28%)
Gene name: Ngly1
Sequence domains: PNGase C-terminal domain, mannose-binding module PAW
Structure domains: Peptide N glycanase, PAW domain

Ligands and Environments

Carbohydrate polymer : NEW Components: MAN
Carbohydrate polymer
2 bound ligands:
Ligand ACT 6 x ACT
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P21
Unit cell:
a: 45.706Å b: 41.646Å c: 94.9Å
α: 90° β: 94.89° γ: 90°
R-values:
R R work R free
0.174 0.172 0.208
Expression system: Escherichia coli

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)