6dsr

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==Re-refinement of P. falciparum orotidine 5'-monophosphate decarboxylase==
==Re-refinement of P. falciparum orotidine 5'-monophosphate decarboxylase==
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<StructureSection load='6dsr' size='340' side='right' caption='[[6dsr]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
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<StructureSection load='6dsr' size='340' side='right'caption='[[6dsr]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6dsr]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DSR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DSR FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6dsr]] 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=6DSR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DSR FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene></td></tr>
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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]] 2.597&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2za1|2za1]]</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=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></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=6dsr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dsr OCA], [https://pdbe.org/6dsr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dsr RCSB], [https://www.ebi.ac.uk/pdbsum/6dsr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dsr ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6dsr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dsr OCA], [http://pdbe.org/6dsr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dsr RCSB], [http://www.ebi.ac.uk/pdbsum/6dsr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dsr ProSAT]</span></td></tr>
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</table>
</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q8T6J6_PLAFA Q8T6J6_PLAFA]
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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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.
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The development of antimalarial drugs remains a public health priority, and the orotidine 5'-monophosphate decarboxylase from Plasmodium falciparum (PfOMPDC) has great potential as a drug target. The crystallization of PfOMPDC with substrate bound represents an important advance for structure-based drug-design efforts [Tokuoka et al. (2008), J. Biochem. 143, 69-78]. The complex of the enzyme bound to the substrate OMP (PDB entry 2za1) would be of particular utility in this regard. However, re-refinement of this structure of the Michaelis complex shows that the bound ligand is the product rather than the substrate. Here, the re-refinement of a set of three structures, the apo enzyme and two versions of the product-bound form (PDB entries 2za1, 2za2 and 2za3), is reported. The improved geometry and fit of these structures to the observed electron density will enhance their utility in antimalarial drug design.
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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>
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Re-refinement of Plasmodium falciparum orotidine 5'-monophosphate decarboxylase provides a clearer picture of an important malarial drug target.,Novak WRP, West KHJ, Kirkman LMD, Brandt GS Acta Crystallogr F Struct Biol Commun. 2018 Oct 1;74(Pt 10):664-668. doi:, 10.1107/S2053230X18010610. Epub 2018 Sep 21. PMID:30279319<ref>PMID:30279319</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
</div>
<div class="pdbe-citations 6dsr" style="background-color:#fffaf0;"></div>
<div class="pdbe-citations 6dsr" style="background-color:#fffaf0;"></div>
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==See Also==
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*[[Uridine 5'-monophosphate synthase 3D structures|Uridine 5'-monophosphate synthase 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Orotidine-5'-phosphate decarboxylase]]
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[[Category: Large Structures]]
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[[Category: Brandt, G S]]
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[[Category: Plasmodium falciparum]]
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[[Category: Novak, W R.P]]
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[[Category: Brandt GS]]
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[[Category: Complex]]
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[[Category: Novak WRP]]
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[[Category: Lyase]]
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[[Category: P falciparum]]
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Current revision

Re-refinement of P. falciparum orotidine 5'-monophosphate decarboxylase

PDB ID 6dsr

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