spacer
spacer

PDBsum entry 2ha5

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Hydrolase PDB id
2ha5
Jmol
Contents
Protein chains
535 a.a. *
Ligands
NAG-FUC
NAG
ACT ×2
AT3 ×5
ETM ×4
P6G
Waters ×886
* Residue conservation analysis
PDB id:
2ha5
Name: Hydrolase
Title: Crystal structure of mutant s203a of acetylcholinesterase co with acetylthiocholine
Structure: Acetylcholinesterase. Chain: a, b. Fragment: catalytic domain. Synonym: ache. Engineered: yes. Mutation: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_variant: lambda zap. Expression_system_cell_line: hek 293. Expression_system_cell: human embryonic kidney cells (hek)
Resolution:
2.15Å     R-factor:   0.177     R-free:   0.210
Authors: Y.Bourne,Z.Radic,G.Sulzenbacher,E.Kim,P.Taylor,P.Marchot
Key ref:
Y.Bourne et al. (2006). Substrate and product trafficking through the active center gorge of acetylcholinesterase analyzed by crystallography and equilibrium binding. J Biol Chem, 281, 29256-29267. PubMed id: 16837465 DOI: 10.1074/jbc.M603018200
Date:
12-Jun-06     Release date:   18-Jul-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P21836  (ACES_MOUSE) -  Acetylcholinesterase
Seq:
Struc:
 
Seq:
Struc:
614 a.a.
535 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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 41.18% similarity
+ H(2)O
=
choline
Bound ligand (Het Group name = AT3)
matches with 54.55% 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     extracellular region   17 terms 
  Biological process     synapse assembly   13 terms 
  Biochemical function     carboxylic ester hydrolase activity     9 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M603018200 J Biol Chem 281:29256-29267 (2006)
PubMed id: 16837465  
 
 
Substrate and product trafficking through the active center gorge of acetylcholinesterase analyzed by crystallography and equilibrium binding.
Y.Bourne, Z.Radic, G.Sulzenbacher, E.Kim, P.Taylor, P.Marchot.
 
  ABSTRACT  
 
Hydrolysis of acetylcholine catalyzed by acetylcholinesterase (AChE), one of the most efficient enzymes in nature, occurs at the base of a deep and narrow active center gorge. At the entrance of the gorge, the peripheral anionic site provides a binding locus for allosteric ligands, including substrates. To date, no structural information on substrate entry to the active center from the peripheral site of AChE or its subsequent egress has been reported. Complementary crystal structures of mouse AChE and an inactive mouse AChE mutant with a substituted catalytic serine (S203A), in various complexes with four substrates (acetylcholine, acetylthiocholine, succinyldicholine, and butyrylthiocholine), two non-hydrolyzable substrate analogues (m-(N,N,N-trimethylammonio)-trifluoroacetophenone and 4-ketoamyltrimethylammonium), and one reaction product (choline) were solved in the 2.05-2.65-A resolution range. These structures, supported by binding and inhibition data obtained on the same complexes, reveal the successive positions and orientations of the substrates bound to the peripheral site and proceeding within the gorge toward the active site, the conformations of the presumed transition state for acylation and the acyl-enzyme intermediate, and the positions and orientations of the dissociating and egressing products. Moreover, the structures of the AChE mutant in complexes with acetylthiocholine and succinyldicholine reveal additional substrate binding sites on the enzyme surface, distal to the gorge entry. Hence, we provide a comprehensive set of structural snapshots of the steps leading to the intermediates of catalysis and the potential regulation by substrate binding to various allosteric sites at the enzyme surface.
 
  Selected figure(s)  
 
Figure 1.
FIGURE 1. Overall view of the mAChE subunit. mAChE is viewed down into the gorge with one 4K-TMA molecule (magenta atoms and surface) bound in the active site (labeled AS) and a second 4K-TMA molecule (orange atoms and surface) bound at the PAS (blue Trp^286 and surface). The long loop Cys^69-Cys^96 is in orange and the disulfide bounds in green. The GlcNac moieties linked to Asn^350 on same face as the gorge entrance (bottom) and Asn^464 in the back door region (right) are shown with red oxygens and blue nitrogens. N and C termini are indicated.
Figure 3.
FIGURE 3. Comparison of active site-bound ligands. Overlays of 4K-TMA bound to mAChE (magenta molecule and surface) with ACh (green) docked in TcAChE (PDB entry 2ACE) (A), choline bound to mAChE (magenta molecule and surface) with choline bound to BChE (orange) (entry 1P0M), (B), ATCh bound to the S203Ala mutant (magenta molecule and surface) with BTCh (orange) and soman (blue) bound to BChE (entry 1P0P) (C). Note the Tyr337Ala mutation in BChE.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 29256-29267) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19757206 T.L.Rosenberry (2010).
Strategies to resolve the catalytic mechanism of acetylcholinesterase.
  J Mol Neurosci, 40, 32-39.  
20871620 Y.Z.Li, X.H.Liu, F.Rong, S.Hu, and Z.Y.Sheng (2010).
Carbachol inhibits TNF-α-induced endothelial barrier dysfunction through alpha 7 nicotinic receptors.
  Acta Pharmacol Sin, 31, 1389-1394.  
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.  
19763296 P.W.Elsinghorst, W.Härtig, S.Goldhammer, J.Grosche, and M.Gütschow (2009).
A gorge-spanning, high-affinity cholinesterase inhibitor to explore beta-amyloid plaques.
  Org Biomol Chem, 7, 3940-3946.  
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.  
19325794 C.Oswald, S.H.Smits, E.Bremer, and L.Schmitt (2008).
Microseeding - a powerful tool for crystallizing proteins complexed with hydrolyzable substrates.
  Int J Mol Sci, 9, 1131-1141.  
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.  
18452905 J.M.Bui, and J.Andrew McCammon (2008).
Intrinsic conformational flexibility of acetylcholinesterase.
  Chem Biol Interact, 175, 303-304.  
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.  
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
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.