4UR9

Structure of ligand bound glycosylhydrolase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Discovery of Selective Small-Molecule Activators of a Bacterial Glycoside Hydrolase.

Darby, J.F.Landstrom, J.Roth, C.He, Y.Davies, G.J.Hubbard, R.E.

(2014) Angew.Chem.Int.Ed.Engl. 53: 13419

  • DOI: 10.1002/anie.201407081

  • PubMed Abstract: 
  • Fragment-based approaches are used routinely to discover enzyme inhibitors as cellular tools and potential therapeutic agents. There have been few reports, however, of the discovery of small-molecule enzyme activators. Herein, we describe the discove ...

    Fragment-based approaches are used routinely to discover enzyme inhibitors as cellular tools and potential therapeutic agents. There have been few reports, however, of the discovery of small-molecule enzyme activators. Herein, we describe the discovery and characterization of small-molecule activators of a glycoside hydrolase (a bacterial O-GlcNAc hydrolase). A ligand-observed NMR screen of a library of commercially available fragments identified an enzyme activator which yielded an approximate 90 % increase in kcat /KM  values (kcat =catalytic rate constant; KM =Michaelis constant). This compound binds to the enzyme in close proximity to the catalytic center. Evolution of the initial hits led to improved compounds that behave as nonessential activators effecting both KM  and Vmax  values (Vmax =maximum rate of reaction). The compounds appear to stabilize an active "closed" form of the enzyme. Such activators could offer an orthogonal alternative to enzyme inhibitors for perturbation of enzyme activity in vivo, and could also be used for glycoside hydrolase activation in many industrial processes.


    Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD (UK).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
O-GLCNACASE BT_4395
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
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BK9
Query on BK9

Download SDF File 
Download CCD File 
A, B
4-ethoxyquinazoline
C10 H10 N2 O
KHYIWRGNPLBXDS-UHFFFAOYSA-N
 Ligand Interaction
OAN
Query on OAN

Download SDF File 
Download CCD File 
A, B
O-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRANOSYLIDENE) AMINO-N-PHENYLCARBAMATE
PUGNAc
C15 H19 N3 O7
PBLNJFVQMUMOJY-JXZOILRNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.222 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.486α = 90.00
b = 162.735β = 90.00
c = 223.179γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-02-25
    Type: Initial release