spacer
spacer

PDBsum entry 2c4h

Go to PDB code: 
protein ligands metals links
Hydrolase PDB id
2c4h
Jmol
Contents
Protein chain
533 a.a. *
Ligands
NAG
NDG
PGE ×2
AT3 ×2
ACE
ACT
Metals
_CL ×11
Waters ×948
* Residue conservation analysis
PDB id:
2c4h
Name: Hydrolase
Title: Torpedo californica acetylcholinesterase in complex with 500mm acetylthiocholine
Structure: Acetylcholinesterase. Chain: a. Synonym: ache. Ec: 3.1.1.7
Source: Torpedo californica. Pacific electric ray. Organism_taxid: 7787. Variant: g2 form. Organ: electric organ. Tissue: electroplaque
Resolution:
2.15Å     R-factor:   0.169     R-free:   0.209
Authors: J.P.Colletier,D.Fournier,H.M.Greenblatt,J.L.Sussman, G.Zaccai,I.Silman,M.Weik
Key ref:
J.P.Colletier et al. (2006). Structural insights into substrate traffic and inhibition in acetylcholinesterase. EMBO J, 25, 2746-2756. PubMed id: 16763558 DOI: 10.1038/sj.emboj.7601175
Date:
19-Oct-05     Release date:   14-Jun-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P04058  (ACES_TORCA) -  Acetylcholinesterase
Seq:
Struc:
 
Seq:
Struc:
586 a.a.
533 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
Bound ligand (Het Group name = AT3)
matches with 54.00% similarity
+
acetate
Bound ligand (Het Group name = ACT)
corresponds exactly
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: 10.1038/sj.emboj.7601175 EMBO J 25:2746-2756 (2006)
PubMed id: 16763558  
 
 
Structural insights into substrate traffic and inhibition in acetylcholinesterase.
J.P.Colletier, D.Fournier, H.M.Greenblatt, J.Stojan, J.L.Sussman, G.Zaccai, I.Silman, M.Weik.
 
  ABSTRACT  
 
Acetylcholinesterase (AChE) terminates nerve-impulse transmission at cholinergic synapses by rapid hydrolysis of the neurotransmitter, acetylcholine. Substrate traffic in AChE involves at least two binding sites, the catalytic and peripheral anionic sites, which have been suggested to be allosterically related and involved in substrate inhibition. Here, we present the crystal structures of Torpedo californica AChE complexed with the substrate acetylthiocholine, the product thiocholine and a nonhydrolysable substrate analogue. These structures provide a series of static snapshots of the substrate en route to the active site and identify, for the first time, binding of substrate and product at both the peripheral and active sites. Furthermore, they provide structural insight into substrate inhibition in AChE at two different substrate concentrations. Our structural data indicate that substrate inhibition at moderate substrate concentration is due to choline exit being hindered by a substrate molecule bound at the peripheral site. At the higher concentration, substrate inhibition arises from prevention of exit of acetate due to binding of two substrate molecules within the active-site gorge.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 3D structure of native TcAChE (pdb access code 1EA5), highlighting the catalytic triad in red, Trp84 in the CAS, Trp279 at the PAS, and the bottleneck residue Phe330 in blue.
Figure 8.
Figure 8 Molecular surfaces of the active-site gorge in native TcAChE (A), and in the OTMA/TcAChE (B), 20 mM TCh/TcAChE (C), 20 mM ATCh/TcAChE (D) and 500 mM ATCh/TcAChE (E) complexes. OTMA, ATCh and TCh are shown as yellow sticks, as is the acetyl group on Ser200 in (D, E).
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2006, 25, 2746-2756) copyright 2006.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22278061 K.Haga, A.C.Kruse, H.Asada, T.Yurugi-Kobayashi, M.Shiroishi, C.Zhang, W.I.Weis, T.Okada, B.K.Kobilka, T.Haga, and T.Kobayashi (2012).
Structure of the human M2 muscarinic acetylcholine receptor bound to an antagonist.
  Nature, 482, 547-551.
PDB code: 3uon
  20807084 C.M.Tanarro, and M.Gütschow (2011).
Hyperbolic mixed-type inhibition of acetylcholinesterase by tetracyclic thienopyrimidines.
  J Enzyme Inhib Med Chem, 26, 350-358.  
21190057 J.S.Fraser, and C.J.Jackson (2011).
Mining electron density for functionally relevant protein polysterism in crystal structures.
  Cell Mol Life Sci, 68, 1829-1841.  
21364766 L.Pezzementi, F.Nachon, and A.Chatonnet (2011).
Evolution of Acetylcholinesterase and Butyrylcholinesterase in the Vertebrates: An Atypical Butyrylcholinesterase from the Medaka Oryzias latipes.
  PLoS One, 6, e17396.  
20414900 M.C.Reed, A.Lieb, and H.F.Nijhout (2010).
The biological significance of substrate inhibition: a mechanism with diverse functions.
  Bioessays, 32, 422-429.  
20382997 M.Weik, and J.P.Colletier (2010).
Temperature-dependent macromolecular X-ray crystallography.
  Acta Crystallogr D Biol Crystallogr, 66, 437-446.  
19757206 T.L.Rosenberry (2010).
Strategies to resolve the catalytic mechanism of acetylcholinesterase.
  J Mol Neurosci, 40, 32-39.  
19699221 J.Shenouda, P.Green, and L.Sultatos (2009).
An evaluation of the inhibition of human butyrylcholinesterase and acetylcholinesterase by the organophosphate chlorpyrifos oxon.
  Toxicol Appl Pharmacol, 241, 135-142.  
19292865 M.Pietsch, L.Christian, T.Inhester, S.Petzold, and M.Gütschow (2009).
Kinetics of inhibition of acetylcholinesterase in the presence of acetonitrile.
  FEBS J, 276, 2292-2307.  
19007306 M.Zimmermann, M.S.Westwell, and S.A.Greenfield (2009).
Impact of detergents on the activity of acetylcholinesterase and on the effectiveness of its inhibitors.
  Biol Chem, 390, 19-26.  
19109006 T.Hansmann, B.Sanson, J.Stojan, M.Weik, J.L.Marty, and D.Fournier (2009).
Kinetic insight into the mechanism of cholinesterasterase inhibition by aflatoxin B1 to develop biosensors.
  Biosens Bioelectron, 24, 2119-2124.  
18471807 A.Shafferman, D.Barak, D.Stein, C.Kronman, B.Velan, N.H.Greig, and A.Ordentlich (2008).
Flexibility versus "rigidity" of the functional architecture of AChE active center.
  Chem Biol Interact, 175, 166-172.  
18422651 F.Nachon, J.Stojan, and D.Fournier (2008).
Insights into substrate and product traffic in the Drosophila melanogaster acetylcholinesterase active site gorge by enlarging a back channel.
  FEBS J, 275, 2659-2664.  
18701720 J.P.Colletier, D.Bourgeois, B.Sanson, D.Fournier, J.L.Sussman, I.Silman, and M.Weik (2008).
Shoot-and-Trap: use of specific x-ray damage to study structural protein dynamics by temperature-controlled cryo-crystallography.
  Proc Natl Acad Sci U S A, 105, 11742-11747.
PDB codes: 2vja 2vjb 2vjc 2vjd 2vt6 2vt7
18579127 J.Stojan (2008).
Kinetic evaluation of multiple initial rate data by simultaneous analysis with two equations.
  Chem Biol Interact, 175, 242-248.  
18422653 P.Masson, M.T.Froment, E.Gillon, F.Nachon, O.Lockridge, and L.M.Schopfer (2008).
Kinetic analysis of effector modulation of butyrylcholinesterase-catalysed hydrolysis of acetanilides and homologous esters.
  FEBS J, 275, 2617-2631.  
19006330 T.L.Rosenberry, L.K.Sonoda, S.E.Dekat, B.Cusack, and J.L.Johnson (2008).
Analysis of the reaction of carbachol with acetylcholinesterase using thioflavin T as a coupled fluorescence reporter.
  Biochemistry, 47, 13056-13063.  
18502801 Y.Xu, J.P.Colletier, M.Weik, H.Jiang, J.Moult, I.Silman, and J.L.Sussman (2008).
Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray versus molecular dynamics.
  Biophys J, 95, 2500-2511.  
18007027 J.P.Colletier, A.Royant, A.Specht, B.Sanson, F.Nachon, P.Masson, G.Zaccai, J.L.Sussman, M.Goeldner, I.Silman, D.Bourgeois, and M.Weik (2007).
Use of a 'caged' analogue to study the traffic of choline within acetylcholinesterase by kinetic crystallography.
  Acta Crystallogr D Biol Crystallogr, 63, 1115-1128.
PDB codes: 2v96 2v97 2v98 2va9
17540769 N.Sekulic, M.Konrad, and A.Lavie (2007).
Structural mechanism for substrate inhibition of the adenosine 5'-phosphosulfate kinase domain of human 3'-phosphoadenosine 5'-phosphosulfate synthetase 1 and its ramifications for enzyme regulation.
  J Biol Chem, 282, 22112-22121.
PDB codes: 2pey 2pez
16837465 Y.Bourne, Z.Radic, G.Sulzenbacher, E.Kim, P.Taylor, and P.Marchot (2006).
Substrate and product trafficking through the active center gorge of acetylcholinesterase analyzed by crystallography and equilibrium binding.
  J Biol Chem, 281, 29256-29267.
PDB codes: 2h9y 2ha0 2ha2 2ha3 2ha4 2ha5 2ha6 2ha7
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 code is shown on the right.