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 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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: 10.1038/nsmb1079
  • Primary Citation of Related Structures:  
  • Also Cited By: 2JIW, 2J4G, 2J47

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUCOSAMINIDASE
A, B
716Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)Mutation(s): 0 
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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GLUCOSAMINIDASE
C, D
12N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

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

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NGT
Query on NGT

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Download CCD File 
A, 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
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
C, D
L-PEPTIDE LINKINGC4 H9 N O2

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MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NGTKi: 200 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.185 
  • 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
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-05-08
    Type: Initial release