1CFJ

METHYLPHOSPHONYLATED ACETYLCHOLINESTERASE (AGED) OBTAINED BY REACTION WITH O-ISOPROPYLMETHYLPHOSPHONOFLUORIDATE (GB, SARIN)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.186 

wwPDB Validation   3D Report Full Report



Literature

Crystal structures of aged phosphonylated acetylcholinesterase: nerve agent reaction products at the atomic level.

Millard, C.B.Kryger, G.Ordentlich, A.Greenblatt, H.M.Harel, M.Raves, M.L.Segall, Y.Barak, D.Shafferman, A.Silman, I.Sussman, J.L.

(1999) Biochemistry 38: 7032-7039

  • DOI: 10.1021/bi982678l
  • Primary Citation of Related Structures:  
    2DFP, 1SOM, 1CFJ

  • PubMed Abstract: 
  • Organophosphorus acid anhydride (OP) nerve agents are potent inhibitors which rapidly phosphonylate acetylcholinesterase (AChE) and then may undergo an internal dealkylation reaction (called "aging") to produce an OP-enzyme conjugate that cannot be r ...

    Organophosphorus acid anhydride (OP) nerve agents are potent inhibitors which rapidly phosphonylate acetylcholinesterase (AChE) and then may undergo an internal dealkylation reaction (called "aging") to produce an OP-enzyme conjugate that cannot be reactivated. To understand the basis for irreversible inhibition, we solved the structures of aged conjugates obtained by reaction of Torpedo californica AChE (TcAChE) with diisopropylphosphorofluoridate (DFP), O-isopropylmethylphosponofluoridate (sarin), or O-pinacolylmethylphosphonofluoridate (soman) by X-ray crystallography to 2.3, 2.6, or 2.2 A resolution, respectively. The highest positive difference density peak corresponded to the OP phosphorus and was located within covalent bonding distance of the active-site serine (S200) in each structure. The OP-oxygen atoms were within hydrogen-bonding distance of four potential donors from catalytic subsites of the enzyme, suggesting that electrostatic forces significantly stabilize the aged enzyme. The active sites of aged sarin- and soman-TcAChE were essentially identical and provided structural models for the negatively charged, tetrahedral intermediate that occurs during deacylation with the natural substrate, acetylcholine. Phosphorylation with DFP caused an unexpected movement in the main chain of a loop that includes residues F288 and F290 of the TcAChE acyl pocket. This is the first major conformational change reported in the active site of any AChE-ligand complex, and it offers a structural explanation for the substrate selectivity of AChE.


    Related Citations: 
    • Crystal Structural of "Aged" Phosphorylated and Phosphonylated torpedo californica Acetylcholinesterase
      Millard, C.B., Kryger, G., Ordentlich, A., Harel, M., Raves, M.L., Greenblatt, H.M., Segall, Y., Barak, D., Shafferman, A., Silman, I., Sussman, J.L.
      (1998) Structure And Function Of Cholinesterases And Related Proteins --: 425

    Organizational Affiliation

    Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel. 1imill@sgjs6.weizmann.ac.il



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (ACETYLCHOLINESTERASE)A537Tetronarce californicaMutation(s): 0 
Gene Names: ache
EC: 3.1.1.7
Find proteins for P04058 (Tetronarce californica)
Explore P04058 
Go to UniProtKB:  P04058
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
GB
Query on GB

Download CCD File 
A
METHYLPHOSPHONIC ACID ESTER GROUP
C H5 O3 P
YACKEPLHDIMKIO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.186 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.395α = 90
b = 111.395β = 90
c = 136.623γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-06-25
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary