› 6mdv

X-ray diffraction
2.5Å resolution

Crystal structure of Streptococcus pyogenes endo-beta-N-acetylglucosaminidase (EndoS2) with high-mannose glycan

Released:
DOI: 10.2210/pdb6mdv/pdb
PDB entry 6mdv coloured by chain, front view.
PDB entry 6mdv coloured by chain, side view.
PDB entry 6mdv coloured by chain, top view.
Source organism: Streptococcus pyogenes
Primary publication:
Molecular Basis of Broad Spectrum N-Glycan Specificity and Processing of Therapeutic IgG Monoclonal Antibodies by Endoglycosidase S2.
Klontz EH, Trastoy B, Deredge D, Fields JK, Li C, Orwenyo J, Marina A, Beadenkopf R, Günther S, Flores J, Wintrode PL, Wang LX, Guerin ME, Sundberg EJ
ACS Cent Sci 5 524-538 (2019)
PMID: 30937380

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-197486 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (3 distinct):
Endo-beta-N-acetylglucosaminidase EndoS2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 802 amino acids
Theoretical weight: 90.88 KDa
Source organism: Streptococcus pyogenes
Expression system: Escherichia coli
UniProt:
  • Canonical: T1WGN1 (Residues: 44-843; Coverage: 99%)
Gene name: endoS2
Sequence domains: Endo-beta-N-acetylglucosaminidase F2, Ig-like domain

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
1 bound ligand:
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P212121
Unit cell:
a: 88.966Å b: 105.353Å c: 257.298Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.201 0.198 0.248
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems.
James et al. (2022)
3 more

6 mentions without citation

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