3cak

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{{Seed}}
 
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[[Image:3cak.png|left|200px]]
 
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==X-ray structure of WT PTE with ethyl phosphate==
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The line below this paragraph, containing "STRUCTURE_3cak", creates the "Structure Box" on the page.
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<StructureSection load='3cak' size='340' side='right'caption='[[3cak]], [[Resolution|resolution]] 1.83&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3cak]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Brevundimonas_diminuta Brevundimonas diminuta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CAK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CAK FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.83&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=DPF:DIETHYL+HYDROGEN+PHOSPHATE'>DPF</scene>, <scene name='pdbligand=EFS:ETHYL+DIHYDROGEN+PHOSPHATE'>EFS</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
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{{STRUCTURE_3cak| PDB=3cak | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3cak FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cak OCA], [https://pdbe.org/3cak PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cak RCSB], [https://www.ebi.ac.uk/pdbsum/3cak PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cak ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/OPD_BREDI OPD_BREDI] Has an unusual substrate specificity for synthetic organophosphate triesters and phosphorofluoridates. All of the phosphate triesters found to be substrates are synthetic compounds. The identity of any naturally occurring substrate for the enzyme is unknown. Has no detectable activity with phosphate monoesters or diesters and no activity as an esterase or protease. It catalyzes the hydrolysis of the insecticide paraoxon at a rate approaching the diffusion limit and thus appears to be optimally evolved for utilizing this synthetic substrate.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ca/3cak_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3cak ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The bacterial phosphotriesterase (PTE) from Pseudomonas diminuta catalyzes the hydrolysis of organophosphate esters at rates close to the diffusion limit. X-ray diffraction studies have shown that a binuclear metal center is positioned in the active site of PTE and that this complex is responsible for the activation of the nucleophilic water from solvent. In this paper, the three-dimensional structure of PTE was determined in the presence of the hydrolysis product, diethyl phosphate (DEP), and a product analogue, cacodylate. In the structure of the PTE-diethyl phosphate complex, the DEP product is found symmetrically bridging the two divalent cations. The DEP displaces the hydroxide from solvent that normally bridges the two divalent cations in structures determined in the presence or absence of substrate analogues. One of the phosphoryl oxygen atoms in the PTE-DEP complex is 2.0 A from the alpha-metal ion, while the other oxygen is 2.2 A from the beta-metal ion. The two metal ions are separated by a distance of 4.0 A. A similar structure is observed in the presence of cacodylate. Analogous complexes have previously been observed for the product complexes of isoaspartyl dipeptidase, d-aminoacylase, and dihydroorotase from the amidohydrolase superfamily of enzymes. The experimentally determined structure of the PTE-diethyl phosphate product complex is inconsistent with a recent proposal based upon quantum mechanical/molecular mechanical simulations which postulated the formation of an asymmetrical product complex bound exclusively to the beta-metal ion with a metal-metal separation of 5.3 A. This structure is also inconsistent with a chemical mechanism for substrate hydrolysis that utilizes the bridging hydroxide as a base to abstract a proton from a water molecule loosely associated with the alpha-metal ion. Density functional theory (DFT) calculations support a reaction mechanism that utilizes the bridging hydroxide as the direct nucleophile in the hydrolysis of organophosphate esters by PTE.
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===X-ray structure of WT PTE with ethyl phosphate===
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Structure of diethyl phosphate bound to the binuclear metal center of phosphotriesterase.,Kim J, Tsai PC, Chen SL, Himo F, Almo SC, Raushel FM Biochemistry. 2008 Sep 9;47(36):9497-504. Epub 2008 Aug 15. PMID:18702530<ref>PMID:18702530</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3cak" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_18702530}}, adds the Publication Abstract to the page
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*[[Phosphotriesterase|Phosphotriesterase]]
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(as it appears on PubMed at http://www.pubmed.gov), where 18702530 is the PubMed ID number.
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*[[Phosphotriesterase 3D structures|Phosphotriesterase 3D structures]]
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== References ==
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{{ABSTRACT_PUBMED_18702530}}
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<references/>
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__TOC__
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==About this Structure==
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</StructureSection>
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3CAK is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Brevundimonas_diminuta Brevundimonas diminuta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CAK OCA].
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==Reference==
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<ref group="xtra">PMID:18702530</ref><references group="xtra"/>
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[[Category: Aryldialkylphosphatase]]
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[[Category: Brevundimonas diminuta]]
[[Category: Brevundimonas diminuta]]
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[[Category: Almo, S C.]]
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[[Category: Large Structures]]
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[[Category: Kim, J.]]
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[[Category: Almo SC]]
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[[Category: Raushel, F M.]]
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[[Category: Kim J]]
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[[Category: Tsai, P C.]]
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[[Category: Raushel FM]]
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[[Category: Hydrolase]]
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[[Category: Tsai P-C]]
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[[Category: Membrane]]
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[[Category: Metal-binding]]
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[[Category: Plasmid]]
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[[Category: Protein-product complex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 10:48:48 2009''
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Current revision

X-ray structure of WT PTE with ethyl phosphate

PDB ID 3cak

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