2XJ7 | pdb_00002xj7

BtGH84 in complex with 6-acetamido-6-deoxy-castanospermine

• PDB DOI: https://doi.org/10.2210/pdb2XJ7/pdb

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


• Deposited: 2010-07-02 Released: 2010-09-29 
• Deposition Author(s): He, Y., Davies, G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.239 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Inhibition of O-Glcnacase Using a Potent and Cell-Permeable Inhibitor Does not Induce Insulin Resistance in 3T3-L1 Adipocytes.

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

(2010) Chem Biol 17: 937

• PubMed: 20851343 
• DOI: https://doi.org/10.1016/j.chembiol.2010.07.006
• Primary Citation Related Structures: 
  2XJ7


• PubMed Abstract: 
  

  To probe increased O-GlcNAc levels as an independent mechanism governing insulin resistance in 3T3-L1 adipocytes, a new class of O-GlcNAcase (OGA) inhibitor was studied. 6-Acetamido-6-deoxy-castanospermine (6-Ac-Cas) is a potent inhibitor of OGA. The structure of 6-Ac-Cas bound in the active site of an OGA homolog reveals structural features contributing to its potency. Treatment of 3T3-L1 adipocytes with 6-Ac-Cas increases O-GlcNAc levels in a dose-dependent manner. These increases in O-GlcNAc levels do not induce insulin resistance functionally, measured using a 2-deoxyglucose (2-DOG) uptake assay, or at the molecular level, determined by evaluating levels of phosphorylated IRS-1 and Akt. These results, and others described, provide a structural blueprint for improved inhibitors and collectively suggest that increased O-GlcNAc levels, brought about by inhibition of OGA, does not by itself cause insulin resistance in 3T3-L1 adipocytes.

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Organizational Affiliation: 
• Department of Chemistry, Simon Fraser University, Burnaby, BC, Canada.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 165.17 kDa 
• Atom Count: 10,749 
• Modeled Residue Count: 1,272 
• Deposited Residue Count: 1,432 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-GLCNACASE BT_4395	A, B	716	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GC2	C [auth A], E [auth B]	6-ACETAMIDO-6-DEOXY-CASTANOSPERMINE C10 H18 N2 O4 IHKWXDCSAKJQKM-SRQGCSHVSA-N
CA	D [auth A], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.239 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.493	α = 104.13
b = 93.981	β = 93.88
c = 98.815	γ = 103.13

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
DENZO	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-29 
Deposition Author(s): He, Y., Davies, G.J.

Revision History  

• Version 1.0: 2010-09-29
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description