2pc5: Difference between revisions

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{{Seed}}
[[Image:2pc5.png|left|200px]]


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==Native crystal structure analysis on Arabidopsis dUTPase==
The line below this paragraph, containing "STRUCTURE_2pc5", creates the "Structure Box" on the page.
<StructureSection load='2pc5' size='340' side='right'caption='[[2pc5]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<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>
or leave the SCENE parameter empty for the default display.
</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>
{{STRUCTURE_2pc5|  PDB=2pc5  |  SCENE=  }}
<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>
</table>
== Function ==
[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>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pc/2pc5_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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).


===Native crystal structure analysis on Arabidopsis dUTPase===
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>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2pc5" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_17565183}}, adds the Publication Abstract to the page
*[[DUTPase 3D structures|DUTPase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 17565183 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_17565183}}
__TOC__
 
</StructureSection>
==About this Structure==
2PC5 is a [[Single protein]] structure of sequence from [http://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].
 
==Reference==
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://www.ncbi.nlm.nih.gov/pubmed/17565183 17565183]
[[Category: Arabidopsis thaliana]]
[[Category: Arabidopsis thaliana]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: DUTP diphosphatase]]
[[Category: Bajaj M]]
[[Category: Bajaj, M.]]
[[Category: Moriyama H]]
[[Category: Moriyama, H.]]
[[Category: Arabidopsis]]
[[Category: Dutpase]]
[[Category: Hydrolase]]
[[Category: Magnesium]]
 
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Retrieved from "https://proteopedia.org/2pc5"