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PDBsum entry 1qii

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protein links
Hydrolase PDB id
1qii
Jmol
Contents
Protein chain
532 a.a. *
Waters ×297
* Residue conservation analysis
PDB id:
1qii
Name: Hydrolase
Title: Specific chemical and structural damage at nine time points (point f) caused by intense synchrotron radiation to torpedo californica acetylcholinesterase
Structure: Acetylcholinesterase. Chain: a. Ec: 3.1.1.7
Source: Torpedo californica. Pacific electric ray. Organism_taxid: 7787. Variant: g2 form. Organ: electric organ. Tissue: electroplaque
Resolution:
2.65Å     R-factor:   0.198     R-free:   0.219
Authors: G.Kryger,M.Weik,R.B.G.Ravelli
Key ref:
M.Weik et al. (2000). Specific chemical and structural damage to proteins produced by synchrotron radiation. Proc Natl Acad Sci U S A, 97, 623-628. PubMed id: 10639129 DOI: 10.1073/pnas.97.2.623
Date:
14-Jun-99     Release date:   28-Jan-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P04058  (ACES_TORCA) -  Acetylcholinesterase
Seq:
Struc:
 
Seq:
Struc:
586 a.a.
532 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
+ 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: 10.1073/pnas.97.2.623 Proc Natl Acad Sci U S A 97:623-628 (2000)
PubMed id: 10639129  
 
 
Specific chemical and structural damage to proteins produced by synchrotron radiation.
M.Weik, R.B.Ravelli, G.Kryger, S.McSweeney, M.L.Raves, M.Harel, P.Gros, I.Silman, J.Kroon, J.L.Sussman.
 
  ABSTRACT  
 
Radiation damage is an inherent problem in x-ray crystallography. It usually is presumed to be nonspecific and manifested as a gradual decay in the overall quality of data obtained for a given crystal as data collection proceeds. Based on third-generation synchrotron x-ray data, collected at cryogenic temperatures, we show for the enzymes Torpedo californica acetylcholinesterase and hen egg white lysozyme that synchrotron radiation also can cause highly specific damage. Disulfide bridges break, and carboxyl groups of acidic residues lose their definition. Highly exposed carboxyls, and those in the active site of both enzymes, appear particularly susceptible. The catalytic triad residue, His-440, in acetylcholinesterase, also appears to be much more sensitive to radiation damage than other histidine residues. Our findings have direct practical implications for routine x-ray data collection at high-energy synchrotron sources. Furthermore, they provide a direct approach for studying the radiation chemistry of proteins and nucleic acids at a detailed, structural level and also may yield information concerning putative "weak links" in a given biological macromolecule, which may be of structural and functional significance.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Sequential Fourier maps showing the time course of cleavage of the Cys-254-Cys-265 disulfide bond in TcAChE. Cysteine residues were refined as alanine residues to avoid model bias. (a) 3Fo-2Fc maps, contoured at 1.5 . (b) Fo-Fc maps, contoured at 3 .
Figure 3.
Fig. 3. Histogram showing the increase in B factors for the side chains of the different types of amino acid in TcAChE as a consequence of synchrotron irradiation. The horizontal line indicates the mean increase in side-chain B factors. The numbers along the x-axis show the number of occurrences of each type of amino acid in TcAChE. The individual bars show the average increase in B factor for each type of amino acid for the second data set (B), as compared with the first data set (A), namely (B factor[B] B factor[A])/B factor[A]. Data in this figure, as well as values for increases in B factors mentioned in the text, are derived from models in which the six S atoms of cysteine residues participating in intrachain disulfide linkages were included in the refinement.
 
  Figures were selected by the author.  
 
 
    Author's comment    
 
  The synchrotron "flash" we were using to study the chemical reaction of the acetylcholinesterase (AChE) enzyme was essentially destroying the target in a very specific way. This observation was stunning, it was more like seeing a 'time-series' movie of a simulated animation of chemical processes; but in fact it was the real thing - a direct experimental observation of a bond breaking that, as far as we are aware, was never seen before. To see movies on how synchrotron radiation can rapidly cause specific damage to a proteins, see: http://www.weizmann.ac.il/sb/faculty_pages/Sussman/movies.html.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23254653 E.G.Allan, M.C.Kander, I.Carmichael, and E.F.Garman (2013).
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Energy dependence of site-specific radiation damage in protein crystals.
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Assessment of radiation damage behaviour in a large collection of empirically optimized datasets highlights the importance of unmeasured complicating effects.
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Diffraction data analysis in the presence of radiation damage.
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20382994 G.P.Bourenkov, and A.N.Popov (2010).
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Progress in research into radiation damage in cryo-cooled macromolecular crystals.
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XANES measurements of the rate of radiation damage to selenomethionine side chains.
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Radioprotectant screening for cryocrystallography.
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17301785 T.Zhou, L.Xu, B.Dey, A.J.Hessell, D.Van Ryk, S.H.Xiang, X.Yang, M.Y.Zhang, M.B.Zwick, J.Arthos, D.R.Burton, D.S.Dimitrov, J.Sodroski, R.Wyatt, G.J.Nabel, and P.D.Kwong (2007).
Structural definition of a conserved neutralization epitope on HIV-1 gp120.
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Crystal structures of a family 19 chitinase from Brassica juncea show flexibility of binding cleft loops.
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C3D: a program for the automated centring of cryocooled crystals.
  Acta Crystallogr D Biol Crystallogr, 62, 1348-1357.  
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PDB code: 2i82
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Cryocooling and radiation damage in macromolecular crystallography.
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In-house sulfur SAD phasing: a case study of the effects of data quality and resolution cutoffs.
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Design and activity of cationic fullerene derivatives as inhibitors of acetylcholinesterase.
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Is radiation damage dependent on the dose rate used during macromolecular crystallography data collection?
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PDB codes: 2bxy 2bxz 2by0 2by1 2by2 2by3 2by5 2by6 2by7 2by8 2by9 2bya
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Quantifying X-ray radiation damage in protein crystals at cryogenic temperatures.
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Structure of the inactive variant C60S of Mycobacterium tuberculosis thiol peroxidase.
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PDB code: 1y25
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Experimental determination of the radiation dose limit for cryocooled protein crystals.
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Crystal structures of human cardiac beta-myosin II S2-Delta provide insight into the functional role of the S2 subfragment.
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PDB codes: 2fxm 2fxo
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Current state and prospects of macromolecular crystallography.
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PDB codes: 2bhx 2bi1 2bi2 2bi3 2bi5 2bi9 2bia 2bie 2big
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PDB codes: 1yq9 1yqw 1yrq
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Oxidized and synchrotron cleaved structures of the disulfide redox center in the N-terminal domain of Salmonella typhimurium AhpF.
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PDB codes: 1zyn 1zyp
15840908 C.Nave, and E.F.Garman (2005).
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De novo calcium/sulfur SAD phasing of the human formylglycine-generating enzyme using in-house data.
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PDB code: 1z70
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X-ray damage to the Mn4Ca complex in single crystals of photosystem II: a case study for metalloprotein crystallography.
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Pros and cons of cryocrystallography: should we also collect a room-temperature data set?
  Acta Crystallogr D Biol Crystallogr, 61, 80-87.
PDB codes: 1x6p 1x6q 1x6r 1x6x 1x6y 1x6z
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Improving radiation-damage substructures for RIP.
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PDB codes: 2blo 2blp 2blq 2blr 2blu 2blv 2blw 2blx 2bly 2blz 2bn1 2bn3
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When X-rays modify the protein structure: radiation damage at work.
  Trends Biochem Sci, 30, 213-219.  
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Phasing in the presence of radiation damage.
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Structure of Ecballium elaterium trypsin inhibitor II (EETI-II): a rigid molecular scaffold.
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PDB codes: 1h9h 1h9i 1w7z
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Neutralization of NGF-TrkA receptor interaction by the novel antagonistic anti-TrkA monoclonal antibody MNAC13: a structural insight.
  Proteins, 58, 717-727.
PDB code: 1seq
15146478 E.I.Howard, R.Sanishvili, R.E.Cachau, A.Mitschler, B.Chevrier, P.Barth, V.Lamour, M.Van Zandt, E.Sibley, C.Bon, D.Moras, T.R.Schneider, A.Joachimiak, and A.Podjarny (2004).
Ultrahigh resolution drug design I: details of interactions in human aldose reductase-inhibitor complex at 0.66 A.
  Proteins, 55, 792-804.
PDB code: 1us0
15036861 E.Pechkova, and C.Nicolini (2004).
Protein nanocrystallography: a new approach to structural proteomics.
  Trends Biotechnol, 22, 117-122.  
15274917 J.M.Dias, T.Alves, C.Bonifácio, A.S.Pereira, J.Trincão, D.Bourgeois, I.Moura, and M.J.Romão (2004).
Structural basis for the mechanism of Ca(2+) activation of the di-heme cytochrome c peroxidase from Pseudomonas nautica 617.
  Structure, 12, 961-973.
PDB codes: 1nml 1rz5 1rz6
15159563 L.Govindasamy, R.Reutzel, M.Agbandje-McKenna, and R.McKenna (2004).
Structural determination of a partially hemihedrally twinned actin crystal.
  Acta Crystallogr D Biol Crystallogr, 60, 1040-1047.  
15272167 M.Grininger, R.B.Ravelli, U.Heider, and K.Zeth (2004).
Expression, crystallization and crystallographic analysis of DegS, a stress sensor of the bacterial periplasm.
  Acta Crystallogr D Biol Crystallogr, 60, 1429-1431.  
15159561 M.Schiltz, P.Dumas, E.Ennifar, C.Flensburg, W.Paciorek, C.Vonrhein, and G.Bricogne (2004).
Phasing in the presence of severe site-specific radiation damage through dose-dependent modelling of heavy atoms.
  Acta Crystallogr D Biol Crystallogr, 60, 1024-1031.  
15213381 R.Kort, H.Komori, S.Adachi, K.Miki, and A.Eker (2004).
DNA apophotolyase from Anacystis nidulans: 1.8 A structure, 8-HDF reconstitution and X-ray-induced FAD reduction.
  Acta Crystallogr D Biol Crystallogr, 60, 1205-1213.
PDB codes: 1owl 1owm 1own 1owo 1owp
15333927 R.M.Cardoso, C.H.Silva, A.P.Ulian de Araújo, T.Tanaka, M.Tanaka, and R.C.Garratt (2004).
Structure of the cytosolic Cu,Zn superoxide dismutase from Schistosoma mansoni.
  Acta Crystallogr D Biol Crystallogr, 60, 1569-1578.
PDB codes: 1to4 1to5
15339224 S.Anderson, V.Srajer, and K.Moffat (2004).
Structural heterogeneity of cryotrapped intermediates in the bacterial blue light photoreceptor, photoactive yellow protein.
  Photochem Photobiol, 80, 7.  
15159568 S.Banumathi, P.H.Zwart, U.A.Ramagopal, M.Dauter, and Z.Dauter (2004).
Structural effects of radiation damage and its potential for phasing.
  Acta Crystallogr D Biol Crystallogr, 60, 1085-1093.  
15341736 V.Adam, A.Royant, V.Nivière, F.P.Molina-Heredia, and D.Bourgeois (2004).
Structure of superoxide reductase bound to ferrocyanide and active site expansion upon X-ray-induced photo-reduction.
  Structure, 12, 1729-1740.
PDB codes: 1vzg 1vzh 1vzi
14573949 C.Yang, J.W.Pflugrath, D.A.Courville, C.N.Stence, and J.D.Ferrara (2003).
Away from the edge: SAD phasing from the sulfur anomalous signal measured in-house with chromium radiation.
  Acta Crystallogr D Biol Crystallogr, 59, 1943-1957.  
14573959 D.Borek, W.Minor, and Z.Otwinowski (2003).
Measurement errors and their consequences in protein crystallography.
  Acta Crystallogr D Biol Crystallogr, 59, 2031-2038.  
12777808 K.Diederichs, S.McSweeney, and R.B.Ravelli (2003).
Zero-dose extrapolation as part of macromolecular synchrotron data reduction.
  Acta Crystallogr D Biol Crystallogr, 59, 903-909.  
12517336 P.Sliz, S.C.Harrison, and G.Rosenbaum (2003).
How does radiation damage in protein crystals depend on X-ray dose?
  Structure, 11, 13-19.  
12777765 U.A.Ramagopal, M.Dauter, and Z.Dauter (2003).
Phasing on anomalous signal of sulfurs: what is the limit?
  Acta Crystallogr D Biol Crystallogr, 59, 1020-1027.  
12447907 B.L.Hanson, G.J.Bunick, J.M.Harp, and A.B.Edmundson (2002).
Mcg in 2030: new techniques for atomic position determination of immune complexes.
  J Mol Recognit, 15, 297-305.  
12136136 E.Ennifar, P.Carpentier, J.L.Ferrer, P.Walter, and P.Dumas (2002).
X-ray-induced debromination of nucleic acids at the Br K absorption edge and implications for MAD phasing.
  Acta Crystallogr D Biol Crystallogr, 58, 1262-1268.  
12011453 M.J.Romanowski, R.E.Soccio, J.L.Breslow, and S.K.Burley (2002).
Crystal structure of the Mus musculus cholesterol-regulated START protein 4 (StarD4) containing a StAR-related lipid transfer domain.
  Proc Natl Acad Sci U S A, 99, 6949-6954.
PDB code: 1jss
11914484 T.Ursby, M.Weik, E.Fioravanti, M.Delarue, M.Goeldner, and D.Bourgeois (2002).
Cryophotolysis of caged compounds: a technique for trapping intermediate states in protein crystals.
  Acta Crystallogr D Biol Crystallogr, 58, 607-614.
PDB codes: 1gsi 1gtv
11567163 C.Yang, and J.W.Pflugrath (2001).
Applications of anomalous scattering from S atoms for improved phasing of protein diffraction data collected at Cu Kalpha wavelength.
  Acta Crystallogr D Biol Crystallogr, 57, 1480-1490.  
11264577 H.K.Leiros, S.M.McSweeney, and A.O.Smalås (2001).
Atomic resolution structures of trypsin provide insight into structural radiation damage.
  Acta Crystallogr D Biol Crystallogr, 57, 488-497.
PDB codes: 1hj8 1hj9
11264586 M.Weik, G.Kryger, A.M.Schreurs, B.Bouma, I.Silman, J.L.Sussman, P.Gros, and J.Kroon (2001).
Solvent behaviour in flash-cooled protein crystals at cryogenic temperatures.
  Acta Crystallogr D Biol Crystallogr, 57, 566-573.  
11567086 M.Weik, R.B.Ravelli, I.Silman, J.L.Sussman, P.Gros, and J.Kroon (2001).
Specific protein dynamics near the solvent glass transition assayed by radiation-induced structural changes.
  Protein Sci, 10, 1953-1961.  
11134922 W.R.Rypniewski, P.R.Ostergaard, M.Nørregaard-Madsen, M.Dauter, and K.S.Wilson (2001).
Fusarium oxysporum trypsin at atomic resolution at 100 and 283 K: a study of ligand binding.
  Acta Crystallogr D Biol Crystallogr, 57, 8.
PDB codes: 1fn8 1fy4 1fy5 1gdn 1gdq 1gdu
11053839 L.M.Rice, T.N.Earnest, and A.T.Brunger (2000).
Single-wavelength anomalous diffraction phasing revisited.
  Acta Crystallogr D Biol Crystallogr, 56, 1413-1420.  
  10892800 M.Harel, G.Kryger, T.L.Rosenberry, W.D.Mallender, T.Lewis, R.J.Fletcher, J.M.Guss, I.Silman, and J.L.Sussman (2000).
Three-dimensional structures of Drosophila melanogaster acetylcholinesterase and of its complexes with two potent inhibitors.
  Protein Sci, 9, 1063-1072.
PDB codes: 1dx4 1qo9 1qon
10745008 R.B.Ravelli, and S.M.McSweeney (2000).
The 'fingerprint' that X-rays can leave on structures.
  Structure, 8, 315-328.  
10801499 W.Minor, D.Tomchick, and Z.Otwinowski (2000).
Strategies for macromolecular synchrotron crystallography.
  Structure, 8, R105-R110.  
10713520 W.P.Burmeister (2000).
Structural changes in a cryo-cooled protein crystal owing to radiation damage.
  Acta Crystallogr D Biol Crystallogr, 56, 328-341.
PDB codes: 1dwa 1dwf 1dwg 1dwh 1dwi 1dwj
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