2JGJ | pdb_00002jgj

Crystal structure of mouse acetylcholinesterase inhibited by aged methamidophos


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.244 (Depositor) 
  • R-Value Work: 
    0.214 (Depositor) 
  • R-Value Observed: 
    0.214 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2JGJ

This is version 1.6 of the entry. See complete history

Literature

Crystal Structures of Acetylcholinesterase in Complex with Organophosphorus Compounds Suggest that the Acyl Pocket Modulates the Aging Reaction by Precluding the Formation of the Trigonal Bipyramidal Transition State.

Hornberg, A.Tunemalm, A.-K.Ekstrom, F.

(2007) Biochemistry 46: 4815

  • DOI: https://doi.org/10.1021/bi0621361
  • Primary Citation Related Structures: 
    2JGE, 2JGF, 2JGI, 2JGJ, 2JGK, 2JGL, 2JGM

  • PubMed Abstract: 

    Organophosphorus compounds (OPs), such as nerve agents and a group of insecticides, irreversibly inhibit the enzyme acetylcholinesterase (AChE) by a rapid phosphorylation of the catalytic Ser203 residue. The formed AChE-OP conjugate subsequently undergoes an elimination reaction, termed aging, that results in an enzyme completely resistant to oxime-mediated reactivation by medical antidotes. In this study, we present crystal structures of the non-aged and aged complexes between Mus musculus AChE (mAChE) and the nerve agents sarin, VX, and diisopropyl fluorophosphate (DFP) and the OP-based insecticides methamidophos (MeP) and fenamiphos (FeP). Non-aged conjugates of MeP, sarin, and FeP and aged conjugates of MeP, sarin, and VX are very similar to the noninhibited apo conformation of AChE. A minor structural change in the side chain of His447 is observed in the non-aged conjugate of VX. In contrast, an extensive rearrangement of the acyl loop region (residues 287-299) is observed in the non-aged structure of DFP and in the aged structures of DFP and FeP. In the case of FeP, the relatively large substituents of the phosphorus atom are reorganized during aging, providing a structural support of an aging reaction that proceeds through a nucleophilic attack on the phosphorus atom. The FeP aging rate constant is 14 times lower than the corresponding constant for the structurally related OP insecticide MeP, suggesting that tight steric constraints of the acyl pocket loop preclude the formation of a trigonal bipyramidal intermediate.


  • Organizational Affiliation
    • FOI CBRN Defence and Security, S-901 82 Umeå, Sweden.

Macromolecule Content 

  • Total Structure Weight: 121.48 kDa 
  • Atom Count: 8,607 
  • Modeled Residue Count: 1,071 
  • Deposited Residue Count: 1,098 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ACETYLCHOLINESTERASE
A, B
548Mus musculusMutation(s): 2 
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: 2Go to GlyGen: P21836-1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P6G

Query on P6G



Download:Ideal Coordinates CCD File
F [auth B]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
AE3

Query on AE3



Download:Ideal Coordinates CCD File
E [auth A]2-(2-ETHOXYETHOXY)ETHANOL
C6 H14 O3
XXJWXESWEXIICW-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SVV
Query on SVV
A, B
L-PEPTIDE LINKINGC3 H9 N2 O5 PSER
SVW
Query on SVW
A, B
L-PEPTIDE LINKINGC3 H9 N2 O5 PSER

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.244 (Depositor) 
  • R-Value Work:  0.214 (Depositor) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.25α = 90
b = 111.2β = 90
c = 227.36γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
CCP4phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-17
    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: 2018-01-17
    Changes: Data collection
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.5: 2021-05-12
    Changes: Derived calculations, Structure summary
  • Version 1.6: 2023-12-13
    Changes: Data collection, Database references, Refinement description