2X0H

BtGH84 Michaelis complex

• PDB DOI: https://doi.org/10.2210/pdb2X0H/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides thetaiotaomicron VPI-5482
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-12-08 Released: 2010-01-26 
• Deposition Author(s): He, Y., Davies, G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.226 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 170.51 kDa 
• Atom Count: 11,257 
• Modelled Residue Count: 1,272 
• Deposited Residue Count: 1,474 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-GLCNACASE BT_4395	A, B	737	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0  EC: 3.2.1.52
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
14T	C [auth A], F [auth B]	3,4-difluorophenyl 2-deoxy-2-[(difluoroacetyl)amino]-beta-D-glucopyranoside C14 H15 F4 N O6 YFQSDCPFGCAUBD-GOBQNSBTSA-N
GOL	D [auth A], E [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.226 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.63	α = 90
b = 163.147	β = 90
c = 224.549	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: 2011-09-21
  Changes: Database references, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Derived calculations, Other, Structure summary
• Version 2.1: 2023-12-20
  Changes: Data collection, Database references, Refinement description, Structure summary