6O5S

Room temperature structure of VX-phosphonylated hAChE in complex with oxime reactivator RS-170B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.801 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Productive reorientation of a bound oxime reactivator revealed in room temperature X-ray structures of native and VX-inhibited human acetylcholinesterase.

Gerlits, O.Kong, X.Cheng, X.Wymore, T.Blumenthal, D.K.Taylor, P.Radic, Z.Kovalevsky, A.

(2019) J.Biol.Chem. 294: 10607-10618

  • DOI: 10.1074/jbc.RA119.008725
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Exposure to organophosphorus compounds (OPs) may be fatal if untreated, and a clear and present danger posed by nerve agent OPs has become palpable in recent years. OPs inactivate acetylcholinesterase (AChE) by covalently modifying its catalytic seri ...

    Exposure to organophosphorus compounds (OPs) may be fatal if untreated, and a clear and present danger posed by nerve agent OPs has become palpable in recent years. OPs inactivate acetylcholinesterase (AChE) by covalently modifying its catalytic serine. Inhibited AChE cannot hydrolyze the neurotransmitter acetylcholine leading to its build-up at the cholinergic synapses and creating an acute cholinergic crisis. Current antidotes, including oxime reactivators that attack the OP-AChE conjugate to free the active enzyme, are inefficient. Better reactivators are sought, but their design is hampered by a conformationally rigid portrait of AChE extracted exclusively from 100K X-ray crystallography and scarcity of structural knowledge on human AChE (hAChE). Here, we present room temperature X-ray structures of native and VX-phosphonylated hAChE with an imidazole-based oxime reactivator, RS-170B. We discovered that inhibition with VX triggers substantial conformational changes in bound RS-170B from a 'non-productive' pose (the reactive aldoxime group points away from the VX-bound serine) in the reactivator-only complex to a 'semi-productive' orientation in the VX-modified complex. This observation, supported by concurrent molecular simulations, suggested that the narrow active site gorge of hAChE may be significantly more dynamic than previously thought, allowing RS-170B to reorient while being bound inside the gorge. Furthermore, we found that small molecules can bind in the choline-binding site hindering approach to the phosphorous of VX-bound serine. Our results provide structural and mechanistic perspectives on the reactivation of OP-inhibited hAChE and demonstrate that structural studies at physiologically relevant temperatures can deliver previously overlooked insights applicable for designing next-generation OP antidotes.


    Organizational Affiliation

    Skaggs Sch of Pharmacy/Pharm Scs, 0650, Univ of California, San Diego.,Oak Ridge National Laboratory, United States.,University of Tennessee, Knoxville, United States.,University of Michigan, United States.,The Ohio State University, United States.,Dept. of Pharmacology, 0636, Univ. of California, San Diego, United States.,Department of Pharmacology & Toxicology, University of Utah, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acetylcholinesterase
A, B
550Homo sapiensMutation(s): 0 
Gene Names: ACHE
EC: 3.1.1.7
Find proteins for P22303 (Homo sapiens)
Go to Gene View: ACHE
Go to UniProtKB:  P22303
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LND
Query on LND

Download SDF File 
Download CCD File 
A, B
4-carbamoyl-1-(3-{2-[(E)-(hydroxyimino)methyl]-1H-imidazol-1-yl}propyl)pyridin-1-ium
C13 H16 N5 O2
AEYBMKVDFNSVJO-UHFFFAOYSA-O
 Ligand Interaction
VX
Query on VX

Download SDF File 
Download CCD File 
A, B
O-ETHYLMETHYLPHOSPHONIC ACID ESTER GROUP
C3 H9 O3 P
UFZOPKFMKMAWLU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.801 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.171 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 125.557α = 90.00
b = 125.557β = 90.00
c = 130.861γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
PHASERphasing
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and StrokeUnited States1U01NS083451

Revision History 

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2019-06-12
    Type: Data collection, Database references
  • Version 1.2: 2019-07-17
    Type: Data collection, Database references