2pc5

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(New page: 200px<br /><applet load="2pc5" size="350" color="white" frame="true" align="right" spinBox="true" caption="2pc5, resolution 2.20&Aring;" /> '''Native crystal struc...)
Current revision (10:58, 30 August 2023) (edit) (undo)
 
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[[Image:2pc5.jpg|left|200px]]<br /><applet load="2pc5" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2pc5, resolution 2.20&Aring;" />
 
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'''Native crystal structure analysis on Arabidopsis dUTPase'''<br />
 
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==Overview==
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==Native crystal structure analysis on Arabidopsis dUTPase==
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The deoxyuridine triphosphate nucleotidohydrolase gene from Arabidopsis, thaliana was expressed and the gene product was purified. Crystallization, was performed by the hanging-drop vapour-diffusion method at 298 K using 2, M ammonium sulfate as the precipitant. X-ray diffraction data were, collected to 2.2 A resolution using Cu K alpha radiation. The crystal, belongs to the orthorhombic space group P2(1)2(1)2(1), with unit-cell, parameters a = 69.90, b = 70.86 A, c = 75.55 A. Assuming the presence of a, trimer in the asymmetric unit, the solvent content was 30%, with a V(M) of, 1.8 A3 Da(-1).
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<StructureSection load='2pc5' size='340' side='right'caption='[[2pc5]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2pc5]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PC5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PC5 FirstGlance]. <br>
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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]] 2.2&#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=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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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=2pc5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pc5 OCA], [https://pdbe.org/2pc5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pc5 RCSB], [https://www.ebi.ac.uk/pdbsum/2pc5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pc5 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DUT_ARATH DUT_ARATH] This enzyme is involved in nucleotide metabolism: it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP, preventing uracil incorporation into DNA.<ref>PMID:20227352</ref>
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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/pc/2pc5_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=2pc5 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 deoxyuridine triphosphate nucleotidohydrolase gene from Arabidopsis thaliana was expressed and the gene product was purified. Crystallization was performed by the hanging-drop vapour-diffusion method at 298 K using 2 M ammonium sulfate as the precipitant. X-ray diffraction data were collected to 2.2 A resolution using Cu K alpha radiation. The crystal belongs to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 69.90, b = 70.86 A, c = 75.55 A. Assuming the presence of a trimer in the asymmetric unit, the solvent content was 30%, with a V(M) of 1.8 A3 Da(-1).
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==About this Structure==
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Purification, crystallization and preliminary crystallographic analysis of deoxyuridine triphosphate nucleotidohydrolase from Arabidopsis thaliana.,Bajaj M, Moriyama H Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 May 1;63(Pt, 5):409-11. Epub 2007 Apr 14. PMID:17565183<ref>PMID:17565183</ref>
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2PC5 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] with <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/dUTP_diphosphatase dUTP diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.23 3.6.1.23] Known structural/functional Site: <scene name='pdbsite=AC1:Mg+Binding+Site+For+Residue+A+167'>AC1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PC5 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Purification, crystallization and preliminary crystallographic analysis of deoxyuridine triphosphate nucleotidohydrolase from Arabidopsis thaliana., Bajaj M, Moriyama H, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 May 1;63(Pt, 5):409-11. Epub 2007 Apr 14. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17565183 17565183]
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</div>
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[[Category: Arabidopsis thaliana]]
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<div class="pdbe-citations 2pc5" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: dUTP diphosphatase]]
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[[Category: Bajaj, M.]]
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[[Category: Moriyama, H.]]
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[[Category: MG]]
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[[Category: arabidopsis]]
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[[Category: dutpase]]
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[[Category: hydrolase]]
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[[Category: magnesium]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 13 08:20:15 2008''
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==See Also==
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*[[DUTPase 3D structures|DUTPase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Arabidopsis thaliana]]
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[[Category: Large Structures]]
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[[Category: Bajaj M]]
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[[Category: Moriyama H]]

Current revision

Native crystal structure analysis on Arabidopsis dUTPase

PDB ID 2pc5

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