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PDBsum entry 2j3q

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protein ligands metals links
Hydrolase PDB id
2j3q
Jmol
Contents
Protein chain
534 a.a. *
Ligands
TFL
NAG ×2
NDG
Metals
_MG ×2
Waters ×85
* Residue conservation analysis
PDB id:
2j3q
Name: Hydrolase
Title: Torpedo acetylcholinesterase complexed with fluorophore thioflavin t
Structure: Acetylcholinesterase. Chain: a. Fragment: residues 22-564. Synonym: ache, torpedo acetylcholinesterase. Ec: 3.1.1.7
Source: Torpedo californica. Pacific electric ray. Organism_taxid: 7787
Resolution:
2.80Å     R-factor:   0.199     R-free:   0.257
Authors: M.Harel,B.Cusack,J.L.Johnson,I.Silman,J.L.Sussman, T.L.Rosenberry
Key ref: M.Harel et al. (2008). Crystal structure of thioflavin T bound to the peripheral site of Torpedo californica acetylcholinesterase reveals how thioflavin T acts as a sensitive fluorescent reporter of ligand binding to the acylation site. J Am Chem Soc, 130, 7856-7861. PubMed id: 18512913 DOI: 10.1021/ja7109822
Date:
23-Aug-06     Release date:   04-Sep-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P04058  (ACES_TORCA) -  Acetylcholinesterase
Seq:
Struc:
 
Seq:
Struc:
586 a.a.
534 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.1.7  - Acetylcholinesterase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Acetylcholine + H2O = choline + acetate
Acetylcholine
Bound ligand (Het Group name = NAG)
matches with 41.00% similarity
+ H(2)O
= choline
+ acetate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     synapse   5 terms 
  Biological process     neurotransmitter catabolic process   2 terms 
  Biochemical function     carboxylic ester hydrolase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1021/ja7109822 J Am Chem Soc 130:7856-7861 (2008)
PubMed id: 18512913  
 
 
Crystal structure of thioflavin T bound to the peripheral site of Torpedo californica acetylcholinesterase reveals how thioflavin T acts as a sensitive fluorescent reporter of ligand binding to the acylation site.
M.Harel, L.K.Sonoda, I.Silman, J.L.Sussman, T.L.Rosenberry.
 
  ABSTRACT  
 
Acetylcholinesterase plays a key role in cholinergic synaptic transmission by hydrolyzing the neurotransmitter acetylcholine with one of the highest known catalytic rate constants. Hydrolysis occurs in a narrow and deep gorge that contains two sites of ligand binding: A peripheral site, or P-site, near the gorge entrance that contributes to catalytic efficiency both by transiently trapping substrate molecules as they enter the gorge and by allosterically accelerating the transfer of the substrate acyl group to a serine hydroxyl in an acylation site or A-site at the base of the gorge. Thioflavin T is a useful reporter of ligand interactions with the A-site. It binds specifically to the P-site with fluorescence that is enhanced approximately 1000-fold over that of unbound thioflavin T, and the enhanced fluorescence is quenched 1.5- to 4-fold when another ligand binds to the A-site in a ternary complex. To clarify the structural basis of this advantageous signal change, we here report the X-ray structure of the complex of thioflavin T with Torpedo californica acetylcholinesterase. The two aromatic rings in thioflavin T are coplanar and are packed snugly parallel to the aromatic side chains of Trp279, Tyr334, and Phe330. Overlays of this structure with the crystal structures of Torpedo californica acetylcholinesterase complexes with either edrophonium or m-( N, N, N-trimethylammonio)-2,2,2-trifluoroacetophenone, two small aromatic ligands that bind specifically to the A-site, indicate that the phenyl side chain of Phe330 must rotate to sterically accommodate both thioflavin T and the A-site ligand in the ternary complex. This rotation may allow some relaxation of the strict coplanarity of the aromatic rings in the bound thioflavin T and result in partial quenching of its fluorescence.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21155827 L.Weiner, E.Roth, and I.Silman (2011).
Targeted Oxidation of Torpedo californica Acetylcholinesterase by Singlet Oxygen.
  Photochem Photobiol, 87, 308-316.  
21264414 V.Dounin, A.Constantinof, H.Schulze, T.T.Bachmann, and K.Kerman (2011).
Electrochemical detection of interaction between Thioflavin T and acetylcholinesterase.
  Analyst, 136, 1234-1238.  
21283870 X.Mao, C.Wang, X.Ma, M.Zhang, L.Liu, L.Zhang, L.Niu, Q.Zeng, Y.Yang, and C.Wang (2011).
Molecular level studies on binding modes of labeling molecules with polyalanine peptides.
  Nanoscale, 3, 1592-1599.  
20126745 C.Rodríguez-Rodríguez, A.Rimola, L.Rodríguez-Santiago, P.Ugliengo, A.Alvarez-Larena, H.Gutiérrez-de-Terán, M.Sodupe, and P.González-Duarte (2010).
Crystal structure of thioflavin-T and its binding to amyloid fibrils: insights at the molecular level.
  Chem Commun (Camb), 46, 1156-1158.  
20826442 L.S.Wolfe, M.F.Calabrese, A.Nath, D.V.Blaho, A.D.Miranker, and Y.Xiong (2010).
Protein-induced photophysical changes to the amyloid indicator dye thioflavin T.
  Proc Natl Acad Sci U S A, 107, 16863-16868.
PDB codes: 3myz 3mzt
19757206 T.L.Rosenberry (2010).
Strategies to resolve the catalytic mechanism of acetylcholinesterase.
  J Mol Neurosci, 40, 32-39.  
18602908 T.L.Rosenberry, L.K.Sonoda, S.E.Dekat, B.Cusack, and J.L.Johnson (2008).
Monitoring the reaction of carbachol with acetylcholinesterase by thioflavin T fluorescence and acetylthiocholine hydrolysis.
  Chem Biol Interact, 175, 235-241.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.