2za3: Difference between revisions

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-[[Image:2za3.jpg|left|200px]]<br /><applet load="2za3" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2za3, resolution 2.65&Aring;" />
-'''Crystal Structure of orotidine 5'-monophosphate decarboxylase complexed with uridine 5'-monophosphate from P.falciparum'''<br />
-==Overview==
+==Crystal Structure of orotidine 5'-monophosphate decarboxylase complexed with uridine 5'-monophosphate from P.falciparum==
-Summary Orotidine 5'-monophoshate decarboxylase (OMPDC) catalyzes the, decarboxylation of orotidine 5'-monophosphate (OMP) to uridine, 5'-monophosphate (UMP). Here, we report the X-ray analysis of apo, substrate or product-complex forms of OMPDC from Plasmodium falciparum, (PfOMPDC) at 2.7, 2.65 and 2.65 A, respectively. The structural analysis, provides the substrate recognition mechanism with dynamic structural, changes, as well as the rearrangement of the hydrogen bond array at the, active site. The structural basis of substrate or product binding to, PfOMPDC will help to uncover the decarboxylation mechanism and facilitate, structure-based optimization of antimalarial drugs.
+<StructureSection load='2za3' size='340' side='right'caption='[[2za3]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2za3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Plasmodium_falciparum Plasmodium falciparum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZA3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZA3 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.65&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2za3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2za3 OCA], [https://pdbe.org/2za3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2za3 RCSB], [https://www.ebi.ac.uk/pdbsum/2za3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2za3 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8T6J6_PLAFA Q8T6J6_PLAFA]
+== 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/za/2za3_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=2za3 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Orotidine 5'-monophoshate decarboxylase (OMPDC) catalyses the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP). Here, we report the X-ray analysis of apo, substrate or product-complex forms of OMPDC from Plasmodium falciparum (PfOMPDC) at 2.7, 2.65 and 2.65 A, respectively. The structural analysis provides the substrate recognition mechanism with dynamic structural changes, as well as the rearrangement of the hydrogen bond array at the active site. The structural basis of substrate or product binding to PfOMPDC will help to uncover the decarboxylation mechanism and facilitate structure-based optimization of antimalarial drugs.
-==About this Structure==
+Structural basis for the decarboxylation of orotidine 5'-monophosphate (OMP) by Plasmodium falciparum OMP decarboxylase.,Tokuoka K, Kusakari Y, Krungkrai SR, Matsumura H, Kai Y, Krungkrai J, Horii T, Inoue T J Biochem. 2008 Jan;143(1):69-78. Epub 2007 Nov 1. PMID:17981823<ref>PMID:17981823</ref>
-ZA3 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Plasmodium_falciparum Plasmodium falciparum] with <scene name='pdbligand=U5P:'>U5P</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Orotidine-5'-phosphate_decarboxylase Orotidine-5'-phosphate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23] Known structural/functional Sites: <scene name='pdbsite=AC1:U5p+Binding+Site+For+Residue+A+500'>AC1</scene> and <scene name='pdbsite=AC2:U5p+Binding+Site+For+Residue+B+600'>AC2</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZA3 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Structural basis for the decarboxylation of orotidine 5'-monophosphate (OMP) by Plasmodium falciparum OMP decarboxylase., Tokuoka K, Kusakari Y, Krungkrai SR, Matsumura H, Krungkrai J, Horii T, Inoue T, J Biochem (Tokyo). 2007 Nov 1;. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17981823 17981823]
+</div>
-[[Category: Orotidine-5'-phosphate decarboxylase]]
+<div class="pdbe-citations 2za3" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Uridine 5'-monophosphate synthase 3D structures|Uridine 5'-monophosphate synthase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Plasmodium falciparum]]
-[[Category: Single protein]]
+[[Category: Inoue T]]
-[[Category: Inoue, T.]]
+[[Category: Tokuoka K]]
-[[Category: Tokuoka, K.]]
-[[Category: U5P]]
-[[Category: lyase]]
-[[Category: orotidine 5'-monophosphate decarboxylase]]
-[[Category: plasmodium falciparum]]
-[[Category: pyrimidine biosynthesis]]
-[[Category: uridine 5'-monophosphate]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 13 08:13:34 2008''