5FOO

6-phospho-beta-glucosidase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

Chemoenzymatic Synthesis of 6-Phospho-Cyclophellitol as a Novel Probe of 6-Phospho-Beta-Glucosidases.

Kwan, D.H., Jin, Y., Jiang, J., Chen, H., Kotzler, M.P., Overkleeft, H.S., Davies, G.J., Withers, S.G.

(2016) FEBS Lett 590: 461

  • DOI: https://doi.org/10.1002/1873-3468.12059
  • Primary Citation of Related Structures:  
    5FOO

  • PubMed Abstract: 

    • Covalent, mechanism-based inhibitors of glycosidases are valuable probe molecules for visualizing enzyme activities in complex systems. We, here, describe the chemoenzymatic synthesis of 6-phospho-cyclophellitol and evaluate its behaviour as a mechanism-based inactivator of the Streptococcus pyogenes 6-phospho-β-glucosidase from CAZy family GH1 ...

    Covalent, mechanism-based inhibitors of glycosidases are valuable probe molecules for visualizing enzyme activities in complex systems. We, here, describe the chemoenzymatic synthesis of 6-phospho-cyclophellitol and evaluate its behaviour as a mechanism-based inactivator of the Streptococcus pyogenes 6-phospho-β-glucosidase from CAZy family GH1. We further present the three-dimensional structure of the inactivated enzyme, which reveals the constellation of active site residues responsible for the enzyme's specificity and confirms the covalent nature of the inactivation.

    Organizational Affiliation: 

    Department of Chemistry, University of British Columbia, BC, Canada.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
6-PHOSPHO-BETA-D GLYCOSIDASE
A, B, C, D, E, F
A, B, C, D, E, F
480Streptococcus pyogenes M1 GASMutation(s): 1 
EC: 3.2.1.21 (PDB Primary Data), 3.2.1.86 (PDB Primary Data)
UniProt
Find proteins for Q99YP9 (Streptococcus pyogenes serotype M1)
Explore Q99YP9 
Go to UniProtKB:  Q99YP9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99YP9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JAZ
Query on JAZ
Download Ideal Coordinates CCD File 
BA [auth D],
G [auth A],
IA [auth E],
LA [auth F],
O [auth B],
BA [auth D],
G [auth A],
IA [auth E],
LA [auth F],
O [auth B],
W [auth C]
6-PHOSPHOCYCLOPHELLITOL
C7 H15 O9 P
UJSILGAUEGUBGA-NYLBLOMBSA-N		 Ligand Interaction
TRS
Query on TRS
Download Ideal Coordinates CCD File 
X [auth C]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
AA [auth C],
GA [auth D],
KA [auth E],
M [auth A],
OA [auth F],
AA [auth C],
GA [auth D],
KA [auth E],
M [auth A],
OA [auth F],
U [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
CA [auth D],
DA [auth D],
EA [auth D],
FA [auth D],
H [auth A],
CA [auth D],
DA [auth D],
EA [auth D],
FA [auth D],
H [auth A],
I [auth A],
J [auth A],
JA [auth E],
K [auth A],
L [auth A],
MA [auth F],
NA [auth F],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
Y [auth C],
Z [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
HA [auth D],
N [auth A],
V [auth B]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.017α = 90
b = 109.899β = 92.02
c = 158.5γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-17
    Type: Initial release
  • Version 1.1: 2016-03-02
    Changes: Database references