› 2vtf

X-ray diffraction
1.79Å resolution

X-ray crystal structure of the Endo-beta-N-acetylglucosaminidase from Arthrobacter protophormiae E173Q mutant reveals a TIM barrel catalytic domain and two ancillary domains

Released:
DOI: 10.2210/pdb2vtf/pdb
PDB entry 2vtf coloured by chain, front view.
PDB entry 2vtf coloured by chain, side view.
PDB entry 2vtf coloured by chain, top view.
Source organism: Glutamicibacter protophormiae
Primary publication:
The X-ray crystal structure of an Arthrobacter protophormiae endo-beta-N-acetylglucosaminidase reveals a (beta/alpha)(8) catalytic domain, two ancillary domains and active site residues key for transglycosylation activity.
Ling Z, Suits MD, Bingham RJ, Bruce NC, Davies GJ, Fairbanks AJ, Moir JW, Taylor EJ
J Mol Biol 389 1-9 (2009)
PMID: 19327363

Function and Biology Details

Reaction catalysed: 
Endohydrolysis of the N,N'-diacetylchitobiosyl unit in high-mannose glycopeptides and glycoproteins containing the -(Man(GlcNAc)(2))Asn- structure. One N-acetyl-D-glucosamine residue remains attached to the protein, the rest of the oligosaccharide is released intact.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195606 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glycoside hydrolase family 85 domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 626 amino acids
Theoretical weight: 70.08 KDa
Source organism: Glutamicibacter protophormiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9ZB22 (Residues: 24-645; Coverage: 96%)
Sequence domains: Glycosyl hydrolase family 85
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand B3P 4 x B3P
Ligand PGE 4 x PGE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: P21212
Unit cell:
a: 89.84Å b: 226.76Å c: 68.35Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.166 0.164 0.202
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

6 review citations

Emerging technologies for making glycan-defined glycoproteins.
Wang et al. (2012)
5 more

4 mentions without citation

Sculpting therapeutic monoclonal antibody N-glycans using endoglycosidases.
Trastoy et al. (2022)
3 more