2WZH

BtGH84 D242N in complex with MeUMB-derived oxazoline

• PDB DOI: https://doi.org/10.2210/pdb2WZH/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides thetaiotaomicron VPI-5482
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.227 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Starting Model: experimental

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

• PubMed: 20067256 
• DOI: https://doi.org/10.1021/ja9086769
• Primary Citation of Related Structures:  
  2WZH, 2WZI, 2X0H


• 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-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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 84.92 kDa 
• Atom Count: 4,943 
• Modelled Residue Count: 572 
• Deposited Residue Count: 737 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-GLCNACASE BT_4395	A	737	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 1  EC: 3.2.1.52 (PDB Primary Data), 3.2.1.169 (UniProt)
UniProt
Find proteins for Q89ZI2 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q89ZI2  Go to UniProtKB:  Q89ZI2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NGO	B [auth A]	2-METHYL-4,5-DIHYDRO-(1,2-DIDEOXY-ALPHA-D-GLUCOPYRANOSO)[2,1-D]-1,3-OXAZOLE C8 H14 N O5 PDBSWNMXMILYCQ-PVFLNQBWSA-O
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.227 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 184.76	α = 90
b = 52.29	β = 100.2
c = 86.93	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Database references, Derived calculations, Non-polymer description, Refinement description, Version format compliance
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description