2WZH

BtGH84 D242N in complex with MeUMB-derived oxazoline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Visualizing the Reaction Coordinate of an O-Glcnac Hydrolase

He, Y.Macauley, M.S.Stubbs, K.A.Vocadlo, D.J.Davies, G.J.

(2010) J.Am.Chem.Soc. 132: 1807

  • DOI: 10.1021/ja9086769
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • N-Acetylglucosamine beta-O-linked to serine and threonine residues of nucleocytoplasmic proteins (O-GlcNAc) has been linked to neurodegeneration, cellular stress response, and transcriptional regulation. Removal of O-GlcNAc is catalyzed by O-GlcNAcas ...

    N-Acetylglucosamine beta-O-linked to serine and threonine residues of nucleocytoplasmic proteins (O-GlcNAc) has been linked to neurodegeneration, cellular stress response, and transcriptional regulation. Removal of O-GlcNAc is catalyzed by O-GlcNAcase (OGA) using a substrate-assisted catalytic mechanism. Here we define the reaction coordinate using chemical approaches and directly observe both a Michaelis complex and the oxazoline intermediate.


    Organizational Affiliation

    York Structural Biology laboratory, Department of Chemistry, The University of York, YO10 5YW, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
O-GLCNACASE BT_4395
A
737Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)Mutation(s): 1 
EC: 3.2.1.169
Find proteins for Q89ZI2 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482))
Go to UniProtKB:  Q89ZI2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NGO
Query on NGO

Download SDF File 
Download CCD File 
A
2-METHYL-4,5-DIHYDRO-(1,2-DIDEOXY-ALPHA-D-GLUCOPYRANOSO)[2,1-D]-1,3-OXAZOLE
N-ACETYLGLUCOSAMINE-OXAZOLINIUM ION INTERMEDIATE
C8 H14 N O5
PDBSWNMXMILYCQ-PVFLNQBWSA-O
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 184.760α = 90.00
b = 52.290β = 100.20
c = 86.930γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-11-30 
  • Released Date: 2010-01-26 
  • Deposition Author(s): He, Y., Davies, G.J.

Revision History 

  • Version 1.0: 2010-01-26
    Type: Initial release
  • Version 1.1: 2011-10-26
    Type: Database references, Derived calculations, Non-polymer description, Refinement description, Version format compliance