1W9D | pdb_00001w9d

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

• PDB DOI: https://doi.org/10.2210/pdb1W9D/pdb

• Classification: HYDROLASE
• Organism(s): Sinapis alba
• Mutation(s): No 


• Deposited: 2004-10-08 Released: 2005-05-19 
• Deposition Author(s): Bourderioux, A., Lefoix, M., Gueyrard, D., Tatibouet, A., Cottaz, S., Arzt, S., Burmeister, W.P., Rollin, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.195 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

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

• PubMed: 15889170 
• DOI: https://doi.org/10.1039/b502990b
• Primary Citation Related Structures: 
  1W9B, 1W9D


• 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 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 62.31 kDa 
• Atom Count: 5,112 
• Modeled Residue Count: 499 
• Deposited Residue Count: 501 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCOSIDASE	A [auth M]	501	Sinapis alba	Mutation(s): 0  EC: 3.2.3.1 (PDB Primary Data), 3.2.1.147 (UniProt)
UniProt
Find proteins for P29736 (Sinapis alba) Explore P29736  Go to UniProtKB:  P29736
Glycosylation
Glycosylation Sites: 9

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B [auth A], E [auth D]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-xylopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth B]	5		N-Glycosylation
Glycosylation Resources
GlyTouCan: G06206UV GlyCosmos: G06206UV GlyGen: G06206UV

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth C]	7		N-Glycosylation
Glycosylation Resources
GlyTouCan: G26295XE GlyCosmos: G26295XE GlyGen: G26295XE

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SEH	L [auth M]	S-BENZYL PHENYLACETOTHIOHYDROXIMATE-O-SULFATE C10 H13 N O4 S2 VZFUNHITNWTQFU-KHPPLWFESA-N
NAG	F [auth M], G [auth M], H [auth M], I [auth M], J [auth M], K [auth M]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	N [auth M], O [auth M], P [auth M], Q [auth M]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	R [auth M], S [auth M], T [auth M]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	M	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.195 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.3	α = 90
b = 137.2	β = 90
c = 80.6	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-05-19 
Deposition Author(s): Bourderioux, A., Lefoix, M., Gueyrard, D., Tatibouet, A., Cottaz, S., Arzt, S., Burmeister, W.P., Rollin, P.

Revision History  

• Version 1.0: 2005-05-19
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-10-23
  Changes: Structure summary