1W9D

S. alba myrosinase in complex with S-ethyl phenylacetothiohydroximate- O-sulfate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The Glucosinolate-Myrosinase System. New Insights Into Enzyme-Substrate Interactions by Use of Simplified Inhibitors

Bourderioux, A.Lefoix, M.Gueyrard, D.Tatibouet, A.Cottaz, S.Arzt, S.Burmeister, W.P.Rollin, P.

(2005) Org.Biomol.Chem. 3: 1872

  • DOI: 10.1039/b502990b
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Myrosinase, a thioglucoside glucohydrolase, is the only enzyme able to hydrolyse glucosinolates, a unique family of molecules bearing an anomeric O-sulfated thiohydroximate function. Non-hydrolysable myrosinase inhibitors have been devised and studie ...

    Myrosinase, a thioglucoside glucohydrolase, is the only enzyme able to hydrolyse glucosinolates, a unique family of molecules bearing an anomeric O-sulfated thiohydroximate function. Non-hydrolysable myrosinase inhibitors have been devised and studied for their biological interaction. Diverse modifications of the O-sulfate moiety did not result in a significant inhibitory effect, whereas replacing the D-glucopyrano residue by its carba-analogue allowed inhibition to take place. X-Ray experiments carried out after soaking allowed for the first time inclusion of a non-hydrolysable inhibitor inside the enzymatic pocket. Structural tuning of the aglycon part in its pocket is being used as a guide for the development of simplified and more potent inhibitors.


    Related Citations: 
    • High Resolution X-Ray Crystallography Shows that Ascorbate is a Cofactor for Myrosinase and Substitutes for the Function of the Catalytic Base
      Burmeister, W.P.,Cottaz, S.,Rollin, P.,Vasella, A.,Henrissat, B.
      (2000) J.Biol.Chem. 275: 39385


    Organizational Affiliation

    Institut de Chimie Organique et Analytique (ICOA), UMR 6005, Université d'Orléans, BP 6759, F-45067, Orléans Cedex 2, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYCOSIDASE
M
501Sinapis albaMutation(s): 0 
EC: 3.2.1.147
Find proteins for P29736 (Sinapis alba)
Go to UniProtKB:  P29736
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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M
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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M
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
SEH
Query on SEH

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M
S-BENZYL PHENYLACETOTHIOHYDROXIMATE-O-SULFATE
ETHYL (1E)-2-PHENYL-N-(SULFOOXY)ETHANIMIDOTHIOATE
C10 H13 N O4 S2
VZFUNHITNWTQFU-KHPPLWFESA-N
 Ligand Interaction
GOL
Query on GOL

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M
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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M
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

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M
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

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M
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

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M
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
XYP
Query on XYP

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M
BETA-D-XYLOPYRANOSE
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SEHIC50: 580000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.189 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 135.300α = 90.00
b = 137.200β = 90.00
c = 80.600γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-05-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2019-05-08
    Type: Data collection, Derived calculations, Experimental preparation, Other