› 6kpo

X-ray diffraction
2.36Å resolution

Crystal Structure of endo-beta-N-acetylglucosaminidase from Cordyceps militaris D154N/E156Q mutant in complex with fucosyl-N-acetylglucosamine-Asn

Released:
DOI: 10.2210/pdb6kpo/pdb
PDB entry 6kpo coloured by chain, front view.
PDB entry 6kpo coloured by chain, side view.
PDB entry 6kpo coloured by chain, top view.
Source organism: Cordyceps militaris CM01
Primary publication:
Structural basis for the specific cleavage of core-fucosylated N-glycans by endo-β-N-acetylglucosaminidase from the fungus Cordyceps militaris.
Seki H, Huang Y, Arakawa T, Yamada C, Kinoshita T, Iwamoto S, Higuchi Y, Takegawa K, Fushinobu S
J Biol Chem 294 17143-17154 (2019)
PMID: 31548313

Function and Biology Details

Reaction catalysed: 
Random endo-hydrolysis of N-acetyl-beta-D-glucosaminide (1->4)-beta-linkages in chitin and chitodextrins
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-124352 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
GH18 domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 303 amino acids
Theoretical weight: 33.4 KDa
Source organism: Cordyceps militaris CM01
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: G3JPF7 (Residues: 20-315; Coverage: 100%)
Gene name: CCM_08020

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
3 bound ligands:
Ligand PGE 1 x PGE
Ligand PEG 2 x PEG
Ligand ASN 1 x ASN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P65
Unit cell:
a: 105.912Å b: 105.912Å c: 62.217Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.188 0.185 0.236
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Potential Applications of Endo-β-N-Acetylglucosaminidases From Bifidobacterium longum Subspecies infantis in Designing Value-Added, Next-Generation Infant Formulas.
Duman et al. (2021)
1 more

2 mentions without citation

Structural basis for the specific cleavage of core-fucosylated N-glycans by endo-β-N-acetylglucosaminidase from the fungus Cordyceps militaris.
Seki et al. (2019)
1 more