1v0t

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[[Image:1v0t.png|left|200px]]
 
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==Phospholipase D from Streptomyces sp. strain PMF soaked with the product glycerophosphate==
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The line below this paragraph, containing "STRUCTURE_1v0t", creates the "Structure Box" on the page.
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<StructureSection load='1v0t' size='340' side='right'caption='[[1v0t]], [[Resolution|resolution]] 1.53&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'>[[1v0t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_sp._PMF Streptomyces sp. PMF]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V0T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V0T 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]] 1.53&#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=PO3:PHOSPHITE+ION'>PO3</scene></td></tr>
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{{STRUCTURE_1v0t| PDB=1v0t | 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=1v0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v0t OCA], [https://pdbe.org/1v0t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v0t RCSB], [https://www.ebi.ac.uk/pdbsum/1v0t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v0t ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/P84147_STRSM P84147_STRSM]
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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/v0/1v0t_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=1v0t 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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Almost all enzyme-catalysed phosphohydrolytic or phosphoryl transfer reactions proceed through a five-coordinated phosphorus transition state. This is also true for the phospholipase D superfamily of enzymes, where the active site usually is made up of two identical sequence repeats of an HKD motif, positioned around an approximate 2-fold axis, where the histidine and lysine residues are essential for catalysis. An almost complete reaction pathway has been elucidated by a series of experiments where crystals of phospholipase D from Streptomyces sp. strain PMF (PLD(PMF)) were soaked for different times with (i) a soluble poor, short-chained phospholipid substrate and (ii) with a product. The various crystal structures were determined to a resolution of 1.35-1.75 A for the different time-steps. Both substrate and product-structures were determined in order to identify the different reaction states and to examine if the reaction actually terminated on formation of phosphatidic acid (the true product of phospholipase D action) or could proceed even further. The results presented support the theory that the phospholipase D superfamily shares a common reaction mechanism, although different family members have very different substrate preferences and perform different catalytic reactions. Results also show that the reaction proceeds via a phosphohistidine intermediate and provide unambiguous identification of a catalytic water molecule, ideally positioned for apical attack on the phosphorus and consistent with an associative in-line phosphoryl transfer reaction. In one of the experiments an apparent five-coordinate phosphorus transition state is observed.
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===PHOSPHOLIPASE D FROM STREPTOMYCES SP. STRAIN PMF SOAKED WITH THE PRODUCT GLYCEROPHOSPHATE===
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The reaction mechanism of phospholipase D from Streptomyces sp. strain PMF. Snapshots along the reaction pathway reveal a pentacoordinate reaction intermediate and an unexpected final product.,Leiros I, McSweeney S, Hough E J Mol Biol. 2004 Jun 11;339(4):805-20. PMID:15165852<ref>PMID:15165852</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 1v0t" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_15165852}}, adds the Publication Abstract to the page
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*[[Phospholipase D 3D structures|Phospholipase D 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 15165852 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_15165852}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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[[1v0t]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_sp. Streptomyces sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V0T OCA].
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[[Category: Streptomyces sp. PMF]]
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[[Category: Hough E]]
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==Reference==
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[[Category: Leiros I]]
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<ref group="xtra">PMID:15165852</ref><ref group="xtra">PMID:10873862</ref><references group="xtra"/>
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[[Category: McSweeney S]]
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[[Category: Phospholipase D]]
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[[Category: Streptomyces sp.]]
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[[Category: Hough, E.]]
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[[Category: Leiros, I.]]
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[[Category: Mcsweeney, S.]]
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[[Category: Glycerophosphate]]
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[[Category: Hydrolase]]
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[[Category: Phospholipase d]]
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[[Category: Product soak]]
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Current revision

Phospholipase D from Streptomyces sp. strain PMF soaked with the product glycerophosphate

PDB ID 1v0t

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