2OSX

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.121 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and Mechanistic Analyses of endo-Glycoceramidase II, a Membrane-associated Family 5 Glycosidase in the Apo and GM3 Ganglioside-bound Forms.

Caines, M.E.Vaughan, M.D.Tarling, C.A.Hancock, S.M.Warren, R.A.Withers, S.G.Strynadka, N.C.

(2007) J.Biol.Chem. 282: 14300-14308

  • DOI: 10.1074/jbc.M611455200
  • Primary Citation of Related Structures:  2OSW, 2OSY

  • PubMed Abstract: 
  • 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 ce ...

    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.


    Organizational Affiliation

    Departments of Biochemistry and Molecular Biology, Chemistry, and Microbiology, University of British Columbia, Vancouver, British Columbia, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endoglycoceramidase II
A
481Rhodococcus sp.EC: 3.2.1.123
Find proteins for O33853 (Rhodococcus sp.)
Go to UniProtKB:  O33853
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
16C
Query on 16C

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A
N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)PALMITAMIDE
C16-CERAMIDE, N-PALMITOYL-D-ERYTHRO-SPHINGOSINE, (2S,3R,4E)-2-PALMITOYLAMINOOCTADEC-4-ENE-1,3-DIOL, (2S,3R,4E)-2-PALMITOYLAMINO-1,3-OCTADEC-4-ENEDIOL
C34 H67 N O3
YDNKGFDKKRUKPY-TURZORIXSA-N
 Ligand Interaction
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BGC
Query on BGC

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A
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
GAL
Query on GAL

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A
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
SIA
Query on SIA

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A
O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.121 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 77.801α = 90.00
b = 61.984β = 112.25
c = 102.846γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
MOSFLMdata reduction
CCP4data scaling
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-02-27
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance