2CHN

Bacteroides thetaiotaomicron hexosaminidase with O-GlcNAcase activity- NAG-thiazoline complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.226 (Depositor) 
  • R-Value Work: 
    0.185 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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Literature

Structure and Mechanism of a Bacterial B-Glucosaminidase Having O-Glcnacase Activity

Dennis, R.J.Taylor, E.J.Macauley, M.S.Stubbs, K.A.Turkenburg, J.P.Hart, S.J.Black, G.N.Vocadlo, D.J.Davies, G.J.

(2006) Nat Struct Mol Biol 13: 365

  • DOI: https://doi.org/10.1038/nsmb1079
  • Primary Citation of Related Structures:  
    2CHN, 2CHO

  • PubMed Abstract: 

    O-GlcNAc is an abundant post-translational modification of serine and threonine residues of nucleocytoplasmic proteins. This modification, found only within higher eukaryotes, is a dynamic modification that is often reciprocal to phosphorylation. In a manner analogous to phosphatases, a glycoside hydrolase termed O-GlcNAcase cleaves O-GlcNAc from modified proteins. Enzymes with high sequence similarity to human O-GlcNAcase are also found in human pathogens and symbionts. We report the three-dimensional structure of O-GlcNAcase from the human gut symbiont Bacteroides thetaiotaomicron both in its native form and in complex with a mimic of the reaction intermediate. Mutagenesis and kinetics studies show that the bacterial enzyme, very similarly to its human counterpart, operates via an unusual 'substrate-assisted' catalytic mechanism, which will inform the rational design of enzyme inhibitors.


  • Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry, University of York, York Y010 5YW, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GLUCOSAMINIDASE
A, B
716Bacteroides thetaiotaomicron VPI-5482Mutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ89ZI2
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GLUCOSAMINIDASE
C, D
12Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
EC: 3.2.1.52
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NGT
Query on NGT

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B]
3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL
C8 H13 N O4 S
DRHXTSWSUAJOJZ-FMDGEEDCSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
K [auth C],
L [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.226 (Depositor) 
  • R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.714α = 75.34
b = 94.544β = 93.86
c = 99.479γ = 77.07
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NGTClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-08
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Data collection, Database references, Derived calculations, Structure summary