PDBsum entry 2osx

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Hydrolase PDB id
Protein chain
449 a.a. *
_NA ×4
Waters ×615
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Endo-glycoceramidase ii from rhodococcus sp.: Ganglioside gm
Structure: Endoglycoceramidase ii. Chain: a. Engineered: yes. Mutation: yes
Source: Rhodococcus sp.. Organism_taxid: 1831. Strain: m-777. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.10Å     R-factor:   0.122     R-free:   0.139
Authors: M.E.C.Caines,N.C.J.Strynadka
Key ref:
M.E.Caines et al. (2007). Structural and mechanistic analyses of endo-glycoceramidase II, a membrane-associated family 5 glycosidase in the Apo and GM3 ganglioside-bound forms. J Biol Chem, 282, 14300-14308. PubMed id: 17329247 DOI: 10.1074/jbc.M611455200
06-Feb-07     Release date:   27-Feb-07    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
O33853  (O33853_RHOSO) -  Endoglycoceramidase II
490 a.a.
449 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Endoglycosylceramidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Oligoglycosylglucosyl-(1<->1)-ceramide + H2O = ceramide + oligoglycosylglucose
+ H(2)O
Bound ligand (Het Group name = 16C)
matches with 40.62% similarity
Bound ligand (Het Group name = SIA)
matches with 50.00% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     hydrolase activity     4 terms  


    Added reference    
DOI no: 10.1074/jbc.M611455200 J Biol Chem 282:14300-14308 (2007)
PubMed id: 17329247  
Structural and mechanistic analyses of endo-glycoceramidase II, a membrane-associated family 5 glycosidase in the Apo and GM3 ganglioside-bound forms.
M.E.Caines, M.D.Vaughan, C.A.Tarling, S.M.Hancock, R.A.Warren, S.G.Withers, N.C.Strynadka.
endo-Glycoceramidase, a membrane-associated family 5 glycosidase, deviates from the typical polysaccharide substrate specificity of other soluble members of the family, preferentially hydrolyzing glycosidic linkages between the oligosaccharide and ceramide moieties of gangliosides. Here we report the first x-ray crystal structures of an endo-glycoceramidase from Rhodococcus sp., in the apo form, in complex with the ganglioside G(M3) (Svennerholm ganglioside nomenclature (Svennerholm, L. (1964) J. Lipid Res. 5, 145-155)), and trapped as a glycosyl-enzyme intermediate. These snapshots provide the first molecular insight into enzyme recognition and association with gangliosides, revealing the structural adaptations necessary for glycosidase-catalyzed hydrolysis and detailing a novel ganglioside binding topology. Consistent with the chemical duality of the substrate, the active site of endo-glycoceramidase is split into a wide, polar cavity to bind the polyhydroxylated oligosaccharide moiety and a narrow, hydrophobic tunnel to bind the ceramide lipid chains. The specific interactions with the ceramide polar head group manifest a surprising aglycone specificity, an observation substantiated by our kinetic analyses. Collectively, the reported structural and kinetic data provide insight toward rational redesign of the synthetic glycosynthase mutant of endo-glycoceramidase to enable facile synthesis of nonnatural, therapeutically useful gangliosides.
  Selected figure(s)  
Figure 2.
FIGURE 2. a, the structure of the EGC monomer. b, the electrostatic surface potential of EGC (red, electronegative; blue, electropositive; contoured from -15 to 1 kT/e). c, the hydrophobic surface potential of EGC (green, hydrophobic; white, polar). d, the structure of the -(1,4)-glucanase from Bacillus agaradherans, Cel5A (Protein Data Bank code 2A3H). e, the electrostatic surface potential of Cel5A (red, electronegative; blue, electropositive; contoured from -20 to 1 kT/e). Bound ligands, G[M3] (a and b) and cellobiose (d and e), are shown as ball-and-stick representations in yellow.
Figure 3.
FIGURE 3. a, electron density for the bound G[M3].AnmF[o] - DF[c] (36) electron density map, calculated after random model perturbation and refinement with G[M3] atoms omitted, is shown contoured around the G[M3] at 2.5 in red. b, a surface representation depicting the G[M3] binding site. G[M3] is shown as a ball-and-stick representation in yellow, surrounded by its ligands in the active site of EGC. c, a schematic representation of polar, close contacts involved in the binding of G[M3]. Water molecules are represented by gray spheres.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 14300-14308) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20466655 H.Karlsson, A.Halim, and S.Teneberg (2010).
Differentiation of glycosphingolipid-derived glycan structural isomers by liquid chromatography/mass spectrometry.
  Glycobiology, 20, 1103-1116.  
19766528 L.X.Wang, and W.Huang (2009).
Enzymatic transglycosylation for glycoconjugate synthesis.
  Curr Opin Chem Biol, 13, 592-600.  
19521058 O.Kanie, A.Kurimoto, Y.Kanie, S.Daikoku, A.Ohtake, and K.Suzuki (2009).
Analysis of behavior of sodiated sugar hemiacetals under low-energy collision-induced dissociation conditions and application to investigating mutarotation and mechanism of a glycosidase.
  Proc Jpn Acad Ser B Phys Biol Sci, 85, 204-215.  
18443630 F.A.Shaikh, and S.G.Withers (2008).
Teaching old enzymes new tricks: engineering and evolution of glycosidases and glycosyl transferases for improved glycoside synthesis.
  Biochem Cell Biol, 86, 169-177.  
18783340 Y.Kacher, B.Brumshtein, S.Boldin-Adamsky, L.Toker, A.Shainskaya, I.Silman, J.L.Sussman, and A.H.Futerman (2008).
Acid beta-glucosidase: insights from structural analysis and relevance to Gaucher disease therapy.
  Biol Chem, 389, 1361-1369.
PDB code: 2vt0
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