7B2W

Torpedo californica acetylcholinesterase complexed with UO2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Torpedo californica acetylcholinesterase is stabilized by binding of a divalent metal ion to a novel and versatile 4D motif.

Silman, I.Shnyrov, V.L.Ashani, Y.Roth, E.Nicolas, A.Sussman, J.L.Weiner, L.

(2021) Protein Sci 30: 966-981

  • DOI: 10.1002/pro.4061
  • Primary Citation of Related Structures:  
    7B2W, 7B38, 7B8E

  • PubMed Abstract: 
  • Stabilization of Torpedo californica acetylcholinesterase by the divalent cations Ca +2 , Mg +2 and Mn +2 was investigated. All three substantially protect the enzyme from thermal inactivation. Electron paramagnetic resonance revealed one high-affinity binding site for Mn +2 and several much weaker sites ...

    Stabilization of Torpedo californica acetylcholinesterase by the divalent cations Ca +2 , Mg +2 and Mn +2 was investigated. All three substantially protect the enzyme from thermal inactivation. Electron paramagnetic resonance revealed one high-affinity binding site for Mn +2 and several much weaker sites. Differential scanning calorimetry showed a single irreversible thermal transition. All three cations raise both the temperature of the transition and the activation energy, with the transition becoming more cooperative. The crystal structures of the Ca +2 and Mg +2 complexes with Torpedo acetylcholinesterase were solved. A principal binding site was identified. In both cases, it consists of four aspartates (a 4D motif), within which the divalent ion is embedded, together with several waters molecules. It makes direct contact with two of the aspartates, and indirect contact, via waters, with the other two. The 4D motif has been identified in 31 acetylcholinesterase sequences and 28 butyrylcholinesterase sequences. Zebrafish acetylcholinesterase also contains the 4D motif; it, too, is stabilized by divalent metal ions. The ASSAM server retrieved 200 other proteins that display the 4D motif, in many of which it is occupied by a divalent cation. It is a very versatile motif, since, even though tightly conserved in terms of rmsd values, it can contain from one to as many as three divalent metal ions, together with a variable number of waters. This novel motif, which binds primarily divalent metal ions, is shared by a broad repertoire of proteins. This article is protected by copyright. All rights reserved.


    Related Citations: 
    • [Treatment of vitreous hemorrhages. Rare causes].
      Aracil, P.
      (1987) Bull Soc Ophtalmol Fr Spec No: 137
    • Atomic structure of acetylcholinesterase from Torpedo californica: a prototypic acetylcholine-binding protein.
      Sussman, J.L., Harel, M., Frolow, F., Oefner, C., Goldman, A., Toker, L., Silman, I.
      (1991) Science 253: 872

    Organizational Affiliation

    Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AcetylcholinesteraseA537Tetronarce californicaMutation(s): 0 
Gene Names: ache
EC: 3.1.1.7
UniProt
Find proteins for P04058 (Tetronarce californica)
Explore P04058 
Go to UniProtKB:  P04058
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IUM
Query on IUM

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]URANYL (VI) ION
O2 U
IZLHQJIUOZHTLW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.166 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.88α = 90
b = 110.88β = 90
c = 134.67γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MERLOTphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-17
    Type: Initial release
  • Version 1.1: 2021-03-24
    Changes: Database references
  • Version 1.2: 2021-04-21
    Changes: Database references