6O5R

Room temperature structure of binary complex of native hAChE with oxime reactivator RS-170B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.4 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
  • Structures With Same Primary Citation

  • 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 serine ...

    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 "nonproductive" 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 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 antidotes.


    Organizational Affiliation

    the Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 kovalevskyay@ornl.gov.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AcetylcholinesteraseA, B550Homo sapiensMutation(s): 0 
Gene Names: ACHE
EC: 3.1.1.7
Find proteins for P22303 (Homo sapiens)
Explore P22303 
Go to UniProtKB:  P22303
NIH Common Fund Data Resources
PHAROS  P22303
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LND
Query on LND

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
CL
Query on CL

Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.609α = 90
b = 125.609β = 90
c = 131.428γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United States1U01NS083451

Revision History 

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2019-06-12
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-17
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.4: 2020-02-19
    Changes: Derived calculations