1E70

2-F-glucosylated MYROSINASE FROM SINAPIS ALBA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

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

  • DOI: 10.1074/jbc.M006796200
  • Primary Citation of Related Structures:  
  • Also Cited By: 1W9D, 1W9B

  • PubMed Abstract: 

    • Myrosinase, an S-glycosidase, hydrolyzes plant anionic 1-thio-beta-d-glucosides (glucosinolates) considered part of the plant defense system. Although O-glycosidases are ubiquitous, myrosinase is the only known S-glycosidase. Its active site is very ...

    Myrosinase, an S-glycosidase, hydrolyzes plant anionic 1-thio-beta-d-glucosides (glucosinolates) considered part of the plant defense system. Although O-glycosidases are ubiquitous, myrosinase is the only known S-glycosidase. Its active site is very similar to that of retaining O-glycosidases, but one of the catalytic residues in O-glycosidases, a carboxylate residue functioning as the general base, is replaced by a glutamine residue. Myrosinase is strongly activated by ascorbic acid. Several binary and ternary complexes of myrosinase with different transition state analogues and ascorbic acid have been analyzed at high resolution by x-ray crystallography along with a 2-deoxy-2-fluoro-glucosyl enzyme intermediate. One of the inhibitors, d-gluconhydroximo-1,5-lactam, binds simultaneously with a sulfate ion to form a mimic of the enzyme-substrate complex. Ascorbate binds to a site distinct from the glucose binding site but overlapping with the aglycon binding site, suggesting that activation occurs at the second step of catalysis, i.e. hydrolysis of the glycosyl enzyme. A water molecule is placed perfectly for activation by ascorbate and for nucleophilic attack on the covalently trapped 2-fluoro-glucosyl-moiety. Activation of the hydrolysis of the glucosyl enzyme intermediate is further evidenced by the observation that ascorbate enhances the rate of reactivation of the 2-fluoro-glycosyl enzyme, leading to the conclusion that ascorbic acid substitutes for the catalytic base in myrosinase.

    Related Citations: 
    • The Crystal Structures of Sinapis Alba Myrosinase and a Covalent Glycosyl-Enzyme Intermediate Provide Insights Into the Substrate Recognition and Active-Site Machinery of an S-Glycosidase
      Burmeister, W.P.,Cottaz, S.,Driguez, H.,Iori, R.,Palmieri, S.,Henrissat, B.
      (1997) Structure 5: 663

    Organizational Affiliation: 

    European Synchrotron Radiation Facility and Forschungszentrum Jülich, BP 220, F-38043 Grenoble cedex, France. wpb@embl-grenoble.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MYROSINASE MA1
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
G2F
Query on G2F
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M
2-deoxy-2-fluoro-alpha-D-glucopyranose
C6 H11 F O5
ZCXUVYAZINUVJD-UKFBFLRUSA-N
 Ligand Interaction
SO4
Query on SO4
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M
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.169 
  • 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
X-PLORphasing
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2000-08-23 
  • Released Date: 2001-01-05 
  • Deposition Author(s): Burmeister, W.P.
  • This entry supersedes: 2MYR

Revision History 

  • Version 1.0: 2001-01-05
    Type: Initial release
  • Version 1.1: 2011-11-16
    Type: Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 1.2: 2019-05-08
    Type: Data collection, Derived calculations, Experimental preparation, Other