› 2osx

X-ray diffraction
1.1Å resolution

Endo-glycoceramidase II from Rhodococcus sp.: Ganglioside GM3 Complex

Released:
DOI: 10.2210/pdb2osx/pdb
PDB entry 2osx coloured by chain, front view.
PDB entry 2osx coloured by chain, side view.
PDB entry 2osx coloured by chain, top view.
Source organism: Rhodococcus sp.
Primary publication:
Structural and mechanistic analyses of endo-glycoceramidase II, a membrane-associated family 5 glycosidase in the Apo and GM3 ganglioside-bound forms.
Caines ME, Vaughan MD, Tarling CA, Hancock SM, Warren RA, Withers SG, Strynadka NC
J Biol Chem 282 14300-8 (2007)
PMID: 17329247

Function and Biology Details

Reaction catalysed: 
Oligoglycosylglucosyl-(1<->1)-ceramide + H(2)O = ceramide + oligoglycosylglucose
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128508 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Endoglycoceramidase II Chain: A
Molecule details ›
Chain: A
Length: 481 amino acids
Theoretical weight: 52.08 KDa
Source organism: Rhodococcus sp.
Expression system: Escherichia coli
UniProt:
  • Canonical: O33853 (Residues: 31-490; Coverage: 99%)
Sequence domains:
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: BGC, GAL, SIA
Carbohydrate polymer
3 bound ligands:
Ligand NA 4 x NA
Ligand 16C 1 x 16C
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.2
Spacegroup: C2
Unit cell:
a: 77.801Å b: 61.984Å c: 102.846Å
α: 90° β: 112.25° γ: 90°
R-values:
R R work R free
0.122 0.121 0.139
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Enzymatic transglycosylation for glycoconjugate synthesis.
Wang et al. (2009)
4 more

8 mentions without citation

Atomic-resolution conformational analysis of the GM3 ganglioside in a lipid bilayer and its implications for ganglioside-protein recognition at membrane surfaces.
DeMarco et al. (2009)
7 more