3BVU

GOLGI MANNOSIDASE II D204A catalytic nucleophile mutant complex with Methyl(alpha-D-mannopyranosyl)-(1->3)-S-[(alpha-D-mannopyranosyl)-(1->6)]-alpha-D-mannopyranoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.114 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Probing the substrate specificity of Golgi alpha-mannosidase II by use of synthetic oligosaccharides and a catalytic nucleophile mutant.

Zhong, W.Kuntz, D.A.Ember, B.Singh, H.Moremen, K.W.Rose, D.R.Boons, G.J.

(2008) J.Am.Chem.Soc. 130: 8975-8983

  • DOI: 10.1021/ja711248y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Inhibition of Golgi alpha-mannosidase II (GMII), which acts late in the N-glycan processing pathway, provides a route to blocking cancer-induced changes in cell surface oligosaccharide structures. To probe the substrate requirements of GMII, oligosac ...

    Inhibition of Golgi alpha-mannosidase II (GMII), which acts late in the N-glycan processing pathway, provides a route to blocking cancer-induced changes in cell surface oligosaccharide structures. To probe the substrate requirements of GMII, oligosaccharides were synthesized that contained an alpha(1,3)- or alpha(1,6)-linked 1-thiomannoside. Surprisingly, these oligosaccharides were not observed in X-ray crystal structures of native Drosophila GMII (dGMII). However, a mutant enzyme in which the catalytic nucleophilic aspartate was changed to alanine (D204A) allowed visualization of soaked oligosaccharides and led to the identification of the binding site for the alpha(1,3)-linked mannoside of the natural substrate. These studies also indicate that the conformational change of the bound mannoside to a high-energy B 2,5 conformation is facilitated by steric hindrance from, and the formation of strong hydrogen bonds to, Asp204. The observation that 1-thio-linked mannosides are not well tolerated by the catalytic site of dGMII led to the synthesis of a pentasaccharide containing the alpha(1,6)-linked Man of the natural substrate and the beta(1,2)-linked GlcNAc moiety proposed to be accommodated by the extended binding site of the enzyme. A cocrystal structure of this compound with the D204A enzyme revealed the molecular interactions with the beta(1,2)-linked GlcNAc. The structure is consistent with the approximately 80-fold preference of dGMII for the cleavage of substrates containing a nonreducing beta(1,2)-linked GlcNAc. By contrast, the lysosomal mannosidase lacks an equivalent GlcNAc binding site and kinetic analysis indicates oligomannoside substrates without non-reducing-terminal GlcNAc modifications are preferred, suggesting that selective inhibitors for GMII could exploit the additional binding specificity of the GlcNAc binding site.


    Organizational Affiliation

    Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-mannosidase 2
A
1045Drosophila melanogasterMutation(s): 1 
Gene Names: alpha-Man-IIa (GmII)
EC: 3.2.1.114
Find proteins for Q24451 (Drosophila melanogaster)
Go to UniProtKB:  Q24451
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MRD
Query on MRD

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Download CCD File 
A
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
WZ2
Query on WZ2

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Download CCD File 
A
methyl alpha-D-mannopyranosyl-(1->3)-[alpha-D-mannopyranosyl-(1->6)]-3-thio-alpha-D-mannopyranoside
Methyl(alpha-D-mannopyranosyl)-(1->3)-S-[(alpha-D-mannopyranosyl)-(1->6)]-alpha-D-mannopyranoside
C19 H34 O15 S
MECMOIIFPKBROO-OINXDFOBSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.114 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 68.992α = 90.00
b = 109.786β = 90.00
c = 139.049γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
PDB_EXTRACTdata extraction
ADSCdata collection
SHELXL-97refinement
DENZOdata reduction
SHELXrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Advisory, Refinement description