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PDBsum entry 2v97

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protein ligands metals links
Hydrolase PDB id
2v97
Jmol
Contents
Protein chains
528 a.a. *
Ligands
CFQ ×4
NAG ×4
Metals
_CL
Waters ×1943
* Residue conservation analysis
PDB id:
2v97
Name: Hydrolase
Title: Structure of the unphotolysed complex of tcache with 1-(2- nitrophenyl)-2,2,2-trifluoroethyl-arsenocholine after a 9 seconds annealing to room temperature
Structure: Acetylcholinesterase. Chain: a, b. 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:
2.40Å     R-factor:   0.207     R-free:   0.272
Authors: J.-P.Colletier,B.Sanson,A.Royant,A.Specht,F.Nachon,P.Masson, G.Zaccai,J.L.Sussman,M.Goeldner,I.Silman,D.Bourgeois, M.Weik
Key ref:
J.P.Colletier et al. (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. PubMed id: 18007027 DOI: 10.1107/S0907444907044472
Date:
22-Aug-07     Release date:   20-Nov-07    
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P04058  (ACES_TORCA) -  Acetylcholinesterase
Seq:
Struc:
 
Seq:
Struc:
586 a.a.
528 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: 10.1107/S0907444907044472 Acta Crystallogr D Biol Crystallogr 63:1115-1128 (2007)
PubMed id: 18007027  
 
 
Use of a 'caged' analogue to study the traffic of choline within acetylcholinesterase by kinetic crystallography.
J.P.Colletier, A.Royant, A.Specht, B.Sanson, F.Nachon, P.Masson, G.Zaccai, J.L.Sussman, M.Goeldner, I.Silman, D.Bourgeois, M.Weik.
 
  ABSTRACT  
 
Acetylcholinesterase plays a crucial role in nerve-impulse transmission at cholinergic synapses. The apparent paradox that it displays high turnover despite its active site being buried raises cogent questions as to how the traffic of substrates and products to and from the active site can occur so rapidly in such circumstances. Here, a kinetic crystallography strategy aimed at structurally addressing the issue of product traffic in acetylcholinesterase is presented, in which UV-laser-induced cleavage of a photolabile precursor of the enzymatic product analogue arsenocholine, 'caged' arsenocholine, is performed in a temperature-controlled X-ray crystallography regime. The 'caged' arsenocholine was shown to bind at both the active and peripheral sites of acetylcholinesterase. UV irradiation of a complex with acetylcholinesterase during a brief temperature excursion from 100 K to room temperature is most likely to have resulted in a decrease in occupancy by the caged compound. Microspectrophotometric experiments showed that the caged compound had indeed been photocleaved. It is proposed that a fraction of the arsenocholine molecules released within the crystal had been expelled from both the active and the peripheral sites. Partial q-weighted difference refinement revealed a relative movement of the two domains in acetylcholinesterase after photolysis and the room-temperature excursion, resulting in an increase in the active-site gorge volume of 30% and 35% in monomers A and B of the asymmetric unit, respectively. Moreover, an alternative route to the active-site gorge of the enzyme appeared to open. This structural characterization of acetylcholinesterase 'at work' is consistent with the idea that choline exits from the enzyme after catalysis either via the gorge or via an alternative 'backdoor' trajectory.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 Photocleavage of NPT-AsCh into AsCh and o-nitrosotrifluoromethylacetophenone.
Figure 9.
Figure 9 Opening of a backdoor across the gorge wall of the active-site in monomer A. (a) The Connolly surface of structure 2^AS (red C^ trace and sticks), with structure 2^GS (blue C^ trace and sticks) superimposed for comparison. (b) The Connolly surface of structure 4^AS (red C^ trace and sticks), with structure 4^GS being superimposed for comparison (blue C^ trace and sticks). Residues Tyr70, Asp72, Glu82, Met83, Trp84, Asn85, Trp279 and Phe290 are shown as sticks. The arrow indicates the opening of a channel owing to a conformational change of Trp84 in structure 4^AS.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2007, 63, 1115-1128) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
20382997 M.Weik, and J.P.Colletier (2010).
Temperature-dependent macromolecular X-ray crystallography.
  Acta Crystallogr D Biol Crystallogr, 66, 437-446.  
20119482 A.Specht, F.Bolze, Z.Omran, J.F.Nicoud, and M.Goeldner (2009).
Photochemical tools to study dynamic biological processes.
  HFSP J, 3, 255-264.  
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.  
19015786 A.V.Cherepanov, E.V.Doroshenko, J.Matysik, S.Vries, and H.J.De Groot (2008).
A view on phosphate ester photochemistry by time-resolved solid state NMR. Intramolecular redox reaction of caged ATP.
  Phys Chem Chem Phys, 10, 6820-6828.  
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
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.  
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.