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PDBsum entry 2vja

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
2vja
Jmol
Contents
Protein chains
528 a.a. *
Ligands
NAG ×4
CCD ×4
PGE ×3
Metals
_CL ×4
Waters ×1600
* Residue conservation analysis
PDB id:
2vja
Name: Hydrolase
Title: Torpedo californica acetylcholinesterase in complex with a non hydrolysable substrate analogue, 4-oxo-n,n,n- trimethylpentanaminium - orthorhombic space group - dataset a at 100k
Structure: Acetylcholinesterase. Chain: a, b. Fragment: residues 22-558. 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:
2.30Å     R-factor:   0.195     R-free:   0.254
Authors: J.P.Colletier,D.Bourgeois,D.Fournier,I.Silman,J.L.Sussman, M.Weik
Key ref:
J.P.Colletier et al. (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. PubMed id: 18701720 DOI: 10.1073/pnas.0804828105
Date:
09-Dec-07     Release date:   22-Jul-08    
PROCHECK
Go to PROCHECK summary
 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
Bound ligand (Het Group name = CCD)
matches with 54.00% similarity
+ 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: 10.1073/pnas.0804828105 Proc Natl Acad Sci U S A 105:11742-11747 (2008)
PubMed id: 18701720  
 
 
Shoot-and-Trap: use of specific x-ray damage to study structural protein dynamics by temperature-controlled cryo-crystallography.
J.P.Colletier, D.Bourgeois, B.Sanson, D.Fournier, J.L.Sussman, I.Silman, M.Weik.
 
  ABSTRACT  
 
Although x-ray crystallography is the most widely used method for macromolecular structure determination, it does not provide dynamical information, and either experimental tricks or complementary experiments must be used to overcome the inherently static nature of crystallographic structures. Here we used specific x-ray damage during temperature-controlled crystallographic experiments at a third-generation synchrotron source to trigger and monitor (Shoot-and-Trap) structural changes putatively involved in an enzymatic reaction. In particular, a nonhydrolyzable substrate analogue of acetylcholinesterase, the "off-switch" at cholinergic synapses, was radiocleaved within the buried enzymatic active site. Subsequent product clearance, observed at 150 K but not at 100 K, indicated exit from the active site possibly via a "backdoor." The simple strategy described here is, in principle, applicable to any enzyme whose structure in complex with a substrate analogue is available and, therefore, could serve as a standard procedure in kinetic crystallography studies.
 
  Selected figure(s)  
 
Figure 1.
Structures of ACh, OTMA, and PsCh.
Figure 3.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21525639 C.Rajendran, F.S.Dworkowski, M.Wang, and C.Schulze-Briese (2011).
Radiation damage in room-temperature data acquisition with the PILATUS 6M pixel detector.
  J Synchrotron Radiat, 18, 318-328.  
21525640 D.H.Juers, and M.Weik (2011).
Similarities and differences in radiation damage at 100 K versus 160 K in a crystal of thermolysin.
  J Synchrotron Radiat, 18, 329-337.  
21525638 E.F.Garman, and M.Weik (2011).
Macromolecular crystallography radiation damage research: what's new?
  J Synchrotron Radiat, 18, 313-317.  
20375001 D.A.Jett (2010).
Finding new cures for neurological disorders: a possible fringe benefit of biodefense research?
  Sci Transl Med, 2, 23ps12.  
20382986 E.F.Garman (2010).
Radiation damage in macromolecular crystallography: what is it and why should we care?
  Acta Crystallogr D Biol Crystallogr, 66, 339-351.  
20435910 F.Rao, and M.Karplus (2010).
Protein dynamics investigated by inherent structure analysis.
  Proc Natl Acad Sci U S A, 107, 9152-9157.  
20012211 M.Warkentin, and R.E.Thorne (2010).
Slow cooling and temperature-controlled protein crystallography.
  J Struct Funct Genomics, 11, 85-89.  
20944242 M.Warkentin, and R.E.Thorne (2010).
Glass transition in thaumatin crystals revealed through temperature-dependent radiation-sensitivity measurements.
  Acta Crystallogr D Biol Crystallogr, 66, 1092-1100.  
20382997 M.Weik, and J.P.Colletier (2010).
Temperature-dependent macromolecular X-ray crystallography.
  Acta Crystallogr D Biol Crystallogr, 66, 437-446.  
21070940 P.Carpentier, A.Royant, M.Weik, and D.Bourgeois (2010).
Raman-assisted crystallography suggests a mechanism of X-ray-induced disulfide radical formation and reparation.
  Structure, 18, 1410-1419.
PDB codes: 2xbr 2xbs
20164644 S.Westenhoff, E.Nazarenko, E.Malmerberg, J.Davidsson, G.Katona, and R.Neutze (2010).
Time-resolved structural studies of protein reaction dynamics: a smorgasbord of X-ray approaches.
  Acta Crystallogr A, 66, 207-219.  
19844017 A.A.McCarthy, S.Brockhauser, D.Nurizzo, P.Theveneau, T.Mairs, D.Spruce, M.Guijarro, M.Lesourd, R.B.Ravelli, and S.McSweeney (2009).
A decade of user operation on the macromolecular crystallography MAD beamline ID14-4 at the ESRF.
  J Synchrotron Radiat, 16, 803-812.  
19240324 E.F.Garman, and C.Nave (2009).
Radiation damage in protein crystals examined under various conditions by different methods.
  J Synchrotron Radiat, 16, 129-132.  
19240328 J.McGeehan, R.B.Ravelli, J.W.Murray, R.L.Owen, F.Cipriani, S.McSweeney, M.Weik, and E.F.Garman (2009).
Colouring cryo-cooled crystals: online microspectrophotometry.
  J Synchrotron Radiat, 16, 163-172.  
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.