spacer
spacer

PDBsum entry 2dfp

Go to PDB code: 
protein ligands links
Hydrolase PDB id
2dfp
Jmol
Contents
Protein chain
534 a.a. *
Ligands
NAG-NAG ×2
NAG
MES
Waters ×376
* Residue conservation analysis
PDB id:
2dfp
Name: Hydrolase
Title: X-ray structure of aged di-isopropyl-phosphoro-fluoridate (d to acetylcholinesterase
Structure: Protein (acetylcholinesterase). Chain: a. Other_details: the protein, acetylcholinesterase, was treat the organophosphate, dfp, prior to crystallization.
Source: Torpedo californica. Pacific electric ray. Organism_taxid: 7787. Variant: g2 form. Organ: electric organ. Tissue: electroplaque
Resolution:
2.30Å     R-factor:   0.186     R-free:   0.228
Authors: G.Kryger,C.B.Millard,I.Silman,J.L.Sussman
Key ref:
C.B.Millard et al. (1999). Crystal structures of aged phosphonylated acetylcholinesterase: nerve agent reaction products at the atomic level. Biochemistry, 38, 7032-7039. PubMed id: 10353814 DOI: 10.1021/bi982678l
Date:
07-Dec-98     Release date:   28-Jun-99    
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
* 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 = MES)
matches with 46.15% 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: 10.1021/bi982678l Biochemistry 38:7032-7039 (1999)
PubMed id: 10353814  
 
 
Crystal structures of aged phosphonylated acetylcholinesterase: nerve agent reaction products at the atomic level.
C.B.Millard, G.Kryger, A.Ordentlich, H.M.Greenblatt, M.Harel, M.L.Raves, Y.Segall, D.Barak, A.Shafferman, I.Silman, J.L.Sussman.
 
  ABSTRACT  
 
Organophosphorus acid anhydride (OP) nerve agents are potent inhibitors which rapidly phosphonylate acetylcholinesterase (AChE) and then may undergo an internal dealkylation reaction (called "aging") to produce an OP-enzyme conjugate that cannot be reactivated. To understand the basis for irreversible inhibition, we solved the structures of aged conjugates obtained by reaction of Torpedo californica AChE (TcAChE) with diisopropylphosphorofluoridate (DFP), O-isopropylmethylphosponofluoridate (sarin), or O-pinacolylmethylphosphonofluoridate (soman) by X-ray crystallography to 2.3, 2.6, or 2.2 A resolution, respectively. The highest positive difference density peak corresponded to the OP phosphorus and was located within covalent bonding distance of the active-site serine (S200) in each structure. The OP-oxygen atoms were within hydrogen-bonding distance of four potential donors from catalytic subsites of the enzyme, suggesting that electrostatic forces significantly stabilize the aged enzyme. The active sites of aged sarin- and soman-TcAChE were essentially identical and provided structural models for the negatively charged, tetrahedral intermediate that occurs during deacylation with the natural substrate, acetylcholine. Phosphorylation with DFP caused an unexpected movement in the main chain of a loop that includes residues F288 and F290 of the TcAChE acyl pocket. This is the first major conformational change reported in the active site of any AChE-ligand complex, and it offers a structural explanation for the substrate selectivity of AChE.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20809418 A.Mijares, J.L.Concepción, J.R.Vielma, and R.Portillo (2011).
Immune detection of acetylcholinesterase in subcellular compartments of Trypanosoma evansi.
  Parasitol Res, 108, 1-5.  
21266781 M.Nishizawa, Y.Yabusaki, and M.Kanaoka (2011).
Identification of the catalytic residues of carboxylesterase from Arthrobacter globiformis by diisopropyl fluorophosphate-labeling and site-directed mutagenesis.
  Biosci Biotechnol Biochem, 75, 89-94.  
19715348 C.Gilley, M.MacDonald, F.Nachon, L.M.Schopfer, J.Zhang, J.R.Cashman, and O.Lockridge (2009).
Nerve agent analogues that produce authentic soman, sarin, tabun, and cyclohexyl methylphosphonate-modified human butyrylcholinesterase.
  Chem Res Toxicol, 22, 1680-1688.  
19536291 F.Ekström, A.Hörnberg, E.Artursson, L.G.Hammarström, G.Schneider, and Y.P.Pang (2009).
Structure of HI-6*sarin-acetylcholinesterase determined by X-ray crystallography and molecular dynamics simulation: reactivator mechanism and design.
  PLoS One, 4, e5957.
PDB codes: 2whp 2whq 2whr
19263097 F.Fan, Z.You, Z.Li, J.Cheng, Y.Tang, and Z.Tang (2009).
A butterfly effect: highly insecticidal resistance caused by only a conservative residue mutated of drosophila melanogaster acetylcholinesterase.
  J Mol Model, 15, 1229-1236.  
19217865 F.Gabel, P.Masson, M.T.Froment, B.P.Doctor, A.Saxena, I.Silman, G.Zaccai, and M.Weik (2009).
Direct correlation between molecular dynamics and enzymatic stability: a comparative neutron scattering study of native human butyrylcholinesterase and its "aged" soman conjugate.
  Biophys J, 96, 1489-1494.  
19452557 M.Amitay, and A.Shurki (2009).
The structure of G117H mutant of butyrylcholinesterase: nerve agents scavenger.
  Proteins, 77, 370-377.  
19435302 M.Mihailescu, and H.Meirovitch (2009).
Absolute free energy and entropy of a mobile loop of the enzyme acetylcholinesterase.
  J Phys Chem B, 113, 7950-7964.  
19271773 T.M.Epstein, U.Samanta, S.D.Kirby, D.M.Cerasoli, and B.J.Bahnson (2009).
Crystal structures of brain group-VIII phospholipase A2 in nonaged complexes with the organophosphorus nerve agents soman and sarin.
  Biochemistry, 48, 3425-3435.
PDB codes: 3dt6 3dt8 3dt9
19394314 U.Samanta, S.D.Kirby, P.Srinivasan, D.M.Cerasoli, and B.J.Bahnson (2009).
Crystal structures of human group-VIIA phospholipase A2 inhibited by organophosphorus nerve agents exhibit non-aged complexes.
  Biochem Pharmacol, 78, 420-429.
PDB codes: 3f96 3f97 3f98 3f9c
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.  
18769671 D.Toiber, A.Berson, D.Greenberg, N.Melamed-Book, S.Diamant, and H.Soreq (2008).
N-acetylcholinesterase-induced apoptosis in Alzheimer's disease.
  PLoS ONE, 3, e3108.  
18365110 H.F.Ji, H.Gao, K.R.Buchapudi, X.Yang, X.Xu, and M.K.Schulte (2008).
Microcantilever biosensors based on conformational change of proteins.
  Analyst, 133, 434-443.  
18502412 H.Grigoryan, L.M.Schopfer, C.M.Thompson, A.V.Terry, P.Masson, and O.Lockridge (2008).
Mass spectrometry identifies covalent binding of soman, sarin, chlorpyrifos oxon, diisopropyl fluorophosphate, and FP-biotin to tyrosines on tubulin: a potential mechanism of long term toxicity by organophosphorus agents.
  Chem Biol Interact, 175, 180-186.  
17729287 J.C.Marx, J.Poncin, J.P.Simorre, P.W.Ramteke, and G.Feller (2008).
The noncatalytic triad of alpha-amylases: a novel structural motif involved in conformational stability.
  Proteins, 70, 320-328.  
18707141 S.J.Ding, J.Carr, J.E.Carlson, L.Tong, W.Xue, Y.Li, L.M.Schopfer, B.Li, F.Nachon, O.Asojo, C.M.Thompson, S.H.Hinrichs, P.Masson, and O.Lockridge (2008).
Five tyrosines and two serines in human albumin are labeled by the organophosphorus agent FP-biotin.
  Chem Res Toxicol, 21, 1787-1794.  
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.  
17188226 B.Li, L.M.Schopfer, S.H.Hinrichs, P.Masson, and O.Lockridge (2007).
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry assay for organophosphorus toxicants bound to human albumin at Tyr411.
  Anal Biochem, 361, 263-272.  
17407327 C.D.Fleming, C.C.Edwards, S.D.Kirby, D.M.Maxwell, P.M.Potter, D.M.Cerasoli, and M.R.Redinbo (2007).
Crystal structures of human carboxylesterase 1 in covalent complexes with the chemical warfare agents soman and tabun.
  Biochemistry, 46, 5063-5071.
PDB codes: 2hrq 2hrr
16763558 J.P.Colletier, D.Fournier, H.M.Greenblatt, J.Stojan, J.L.Sussman, G.Zaccai, I.Silman, and M.Weik (2006).
Structural insights into substrate traffic and inhibition in acetylcholinesterase.
  EMBO J, 25, 2746-2756.
PDB codes: 2c4h 2c58 2c5f 2c5g
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
16100272 F.Gabel, M.Weik, P.Masson, F.Renault, D.Fournier, L.Brochier, B.P.Doctor, A.Saxena, I.Silman, and G.Zaccai (2005).
Effects of soman inhibition and of structural differences on cholinesterase molecular dynamics: a neutron scattering study.
  Biophys J, 89, 3303-3311.  
15481087 M.A.Olson (2004).
Modeling loop reorganization free energies of acetylcholinesterase: a comparison of explicit and implicit solvent models.
  Proteins, 57, 645-650.  
15128307 P.Masson, N.Bec, M.T.Froment, F.Nachon, C.Balny, O.Lockridge, and L.M.Schopfer (2004).
Rate-determining step of butyrylcholinesterase-catalyzed hydrolysis of benzoylcholine and benzoylthiocholine. Volumetric study of wild-type and D70G mutant behavior.
  Eur J Biochem, 271, 1980-1990.  
15690493 Y.P.Pang (2004).
Three-dimensional model of a substrate-bound SARS chymotrypsin-like cysteine proteinase predicted by multiple molecular dynamics simulations: catalytic efficiency regulated by substrate binding.
  Proteins, 57, 747-757.
PDB codes: 1p76 2aj5
12794858 E.Henke, U.T.Bornscheuer, R.D.Schmid, and J.Pleiss (2003).
A molecular mechanism of enantiorecognition of tertiary alcohols by carboxylesterases.
  Chembiochem, 4, 485-493.  
12933813 K.M.George, T.Schule, L.E.Sandoval, L.L.Jennings, P.Taylor, and C.M.Thompson (2003).
Differentiation between acetylcholinesterase and the organophosphate-inhibited form using antibodies and the correlation of antibody recognition with reactivation mechanism and rate.
  J Biol Chem, 278, 45512-45518.  
12601798 T.Zeev-Ben-Mordehai, I.Silman, and J.L.Sussman (2003).
Acetylcholinesterase in motion: visualizing conformational changes in crystal structures by a morphing procedure.
  Biopolymers, 68, 395-406.  
12421810 X.Zhu, N.A.Larsen, A.Basran, N.C.Bruce, and I.A.Wilson (2003).
Observation of an arsenic adduct in an acetyl esterase crystal structure.
  J Biol Chem, 278, 2008-2014.
PDB codes: 1lzk 1lzl
12869558 Y.Nicolet, O.Lockridge, P.Masson, J.C.Fontecilla-Camps, and F.Nachon (2003).
Crystal structure of human butyrylcholinesterase and of its complexes with substrate and products.
  J Biol Chem, 278, 41141-41147.
PDB codes: 1p0i 1p0m 1p0p 1p0q
12837382 Y.P.Pang, T.M.Kollmeyer, F.Hong, J.C.Lee, P.I.Hammond, S.P.Haugabouk, and S.Brimijoin (2003).
Rational design of alkylene-linked bis-pyridiniumaldoximes as improved acetylcholinesterase reactivators.
  Chem Biol, 10, 491-502.
PDB codes: 1jga 1jgb 1puv 1puw
12081473 D.Barak, D.Kaplan, A.Ordentlich, N.Ariel, B.Velan, and A.Shafferman (2002).
The aromatic "trapping" of the catalytic histidine is essential for efficient catalysis in acetylcholinesterase.
  Biochemistry, 41, 8245-8252.  
12057683 F.M.Raushel (2002).
Bacterial detoxification of organophosphate nerve agents.
  Curr Opin Microbiol, 5, 288-295.  
12196517 J.Shi, Z.Radic', and P.Taylor (2002).
Inhibitors of different structure induce distinguishing conformations in the omega loop, Cys69-Cys96, of mouse acetylcholinesterase.
  J Biol Chem, 277, 43301-43308.  
11526341 A.Nicolas, F.Ferron, L.Toker, J.L.Sussman, and I.Silman (2001).
Histochemical method for characterization of enzyme crystals: application to crystals of Torpedo californica acetylcholinesterase.
  Acta Crystallogr D Biol Crystallogr, 57, 1348-1350.  
11517229 J.Shi, A.E.Boyd, Z.Radic, and P.Taylor (2001).
Reversibly bound and covalently attached ligands induce conformational changes in the omega loop, Cys69-Cys96, of mouse acetylcholinesterase.
  J Biol Chem, 276, 42196-42204.  
11341926 P.Masson, W.Xie, M.T.Froment, and O.Lockridge (2001).
Effects of mutations of active site residues and amino acids interacting with the Omega loop on substrate activation of butyrylcholinesterase.
  Biochim Biophys Acta, 1544, 166-176.  
11123949 C.Viragh, T.K.Harris, P.M.Reddy, M.A.Massiah, A.S.Mildvan, and I.M.Kovach (2000).
NMR evidence for a short, strong hydrogen bond at the active site of a cholinesterase.
  Biochemistry, 39, 16200-16205.  
10869181 M.Inoue, J.Hiratake, H.Suzuki, H.Kumagai, and K.Sakata (2000).
Identification of catalytic nucleophile of Escherichia coli gamma-glutamyltranspeptidase by gamma-monofluorophosphono derivative of glutamic acid: N-terminal thr-391 in small subunit is the nucleophile.
  Biochemistry, 39, 7764-7771.  
10745008 R.B.Ravelli, and S.M.McSweeney (2000).
The 'fingerprint' that X-rays can leave on structures.
  Structure, 8, 315-328.  
  10631970 R.Arnon, I.Silman, and R.Tarrab-Hazdai (1999).
Acetylcholinesterase of Schistosoma mansoni--functional correlates. Contributed in honor of Professor Hans Neurath's 90th birthday.
  Protein Sci, 8, 2553-2561.  
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.