2WU3

CRYSTAL STRUCTURE OF MOUSE ACETYLCHOLINESTERASE IN COMPLEX WITH FENAMIPHOS AND HI-6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.226 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HI6Click on this verticalbar to view detailsBest fitted NAGClick on this verticalbar to view details

This is version 2.3 of the entry. See complete history


Literature

Crystal Structures of Oxime-Bound Fenamiphos-Acetylcholinesterases: Reactivation Involving Flipping of the His447 Ring to Form a Reactive Glu334-His447-Oxime Triad.

Hornberg, A.Artursson, E.Warme, R.Pang, Y.-P.Ekstrom, F.

(2010) Biochem Pharmacol 79: 507

  • DOI: https://doi.org/10.1016/j.bcp.2009.08.027
  • Primary Citation of Related Structures:  
    2WU3, 2WU4

  • PubMed Abstract: 

    Organophosphorus insecticides and nerve agents inhibit the vital enzyme acetylcholinesterase by covalently bonding to the catalytic serine residue of the enzyme. Oxime-based reactivators, such as [(E)-[1-[(4-carbamoylpyridin-1-ium-1-yl)methoxymethyl]pyridin-2-ylidene]methyl]-oxoazanium dichloride (HI-6) and 1,7-heptylene-bis-N,N'-2-pyridiniumaldoxime dichloride (Ortho-7), restore the organophosphate-inhibited enzymatic activity by cleaving the phosphorous conjugate. In this article, we report the intermolecular interactions between Mus musculus acetylcholinesterase inhibited by the insecticide fenamiphos (fep-mAChE) and HI-6 or Ortho-7 revealed by a combination of crystallography and kinetics. The crystal structures of the two oxime-bound fep-mAChE complexes show that both oximes interact with the peripheral anionic site involving different conformations of Trp286 and different peripheral-site residues (Tyr124 for HI-6 and Tyr72 for Ortho-7). Moreover, residues at catalytic site of the HI-6-bound fep-mAChE complex adopt conformations that are similar to those in the apo mAChE, whereas significant conformational changes are observed for the corresponding residues in the Ortho-7-bound fep-mAChE complex. Interestingly, flipping of the His447 imidazole ring allows the formation of a hydrogen bonding network among the Glu334-His447-Ortho-7 triad, which presumably deprotonates the Ortho-7 oxime hydroxyl group, increases the nucleophilicity of the oxime group, and leads to cleavage of the phosphorous conjugate. These results offer insights into a detailed reactivation mechanism for the oximes and development of improved reactivators.


  • Organizational Affiliation

    Swedish Defence Research Agency, Division of CBRN Defence and Security, S-901 82 Umeå, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ACETYLCHOLINESTERASE
A, B
548Mus musculusMutation(s): 0 
EC: 3.1.1.7
UniProt & NIH Common Fund Data Resources
Find proteins for P21836 (Mus musculus)
Explore P21836 
Go to UniProtKB:  P21836
IMPC:  MGI:87876
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21836
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P21836-1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HI6
Query on HI6

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
4-(AMINOCARBONYL)-1-[({2-[(E)-(HYDROXYIMINO)METHYL]PYRIDINIUM-1-YL}METHOXY)METHYL]PYRIDINIUM
C14 H16 N4 O3
FJZDLOMCEPUCII-UHFFFAOYSA-P
P6G
Query on P6G

Download Ideal Coordinates CCD File 
F [auth A]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CO3
Query on CO3

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B]
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SXE
Query on SXE
A, B
L-PEPTIDE LINKINGC8 H19 N2 O5 PSER
Binding Affinity Annotations 
IDSourceBinding Affinity
HI6 BindingDB:  2WU3 Kd: min: 1.50e+4, max: 2.34e+5 (nM) from 6 assay(s)
IC50: min: 6.36e+5, max: 1.36e+6 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.226 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.76α = 90
b = 111.23β = 90
c = 227.7γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
CCP4phasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HI6Click on this verticalbar to view detailsBest fitted NAGClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-20
    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: 2017-07-12
    Changes: Advisory, Data collection, Derived calculations
  • Version 2.0: 2019-05-15
    Changes: Data collection, Derived calculations, Polymer sequence
  • Version 2.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 2.2: 2021-05-12
    Changes: Derived calculations, Structure summary
  • Version 2.3: 2023-12-20
    Changes: Data collection, Database references, Refinement description