4dl8

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==Crystal structure of Trypanosoma brucei dUTPase with dUMP, planar [AlF3-OPO3] transition state analogue, Mg2+, and Na+==
==Crystal structure of Trypanosoma brucei dUTPase with dUMP, planar [AlF3-OPO3] transition state analogue, Mg2+, and Na+==
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<StructureSection load='4dl8' size='340' side='right' caption='[[4dl8]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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<StructureSection load='4dl8' size='340' side='right'caption='[[4dl8]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4dl8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_(trypanozoon)_brucei Trypanosoma (trypanozoon) brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DL8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DL8 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4dl8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_brucei Trypanosoma brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DL8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DL8 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=AF3:ALUMINUM+FLUORIDE'>AF3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=UMP:2-DEOXYURIDINE+5-MONOPHOSPHATE'>UMP</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]] 1.698&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4dk2|4dk2]], [[4dk4|4dk4]], [[4dkb|4dkb]], [[4dlc|4dlc]]</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=AF3:ALUMINUM+FLUORIDE'>AF3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=UMP:2-DEOXYURIDINE+5-MONOPHOSPHATE'>UMP</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Tb927.7.5160 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5691 Trypanosoma (Trypanozoon) brucei])</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=4dl8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dl8 OCA], [https://pdbe.org/4dl8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dl8 RCSB], [https://www.ebi.ac.uk/pdbsum/4dl8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dl8 ProSAT]</span></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/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] </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=4dl8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dl8 OCA], [http://pdbe.org/4dl8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4dl8 RCSB], [http://www.ebi.ac.uk/pdbsum/4dl8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4dl8 ProSAT]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q57ZH3_TRYB2 Q57ZH3_TRYB2]
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The Tritryps Trypanosoma brucei, T. cruzi and Leishmania donovani are responsible for great morbidity and mortality in developing countries. Their dimeric dUTPases are members of the all-a NTP pyrophosphohydrolase family and represent promising drug targets due to their essential nature and markedly different structural and biochemical properties compared to the trimeric human enzyme. Here we present the structure of the T. brucei enzyme in open and closed conformations. Furthermore, we probe the reaction mechanism through the binding of transition state mimics both in solution and in the crystal. 31P-NMR and tryptophan fluorescence quenching in the presence of AlF3 and MgF3- identified which phosphate is subject to nucleophilic attack by a water molecule. The structures in complex with two transition state analogues confirm that the nucleophilic attack occurs on the b-phosphate in contrast to the a-phosphate in the trimeric enzymes. These results establish the structural basis of catalysis of these important house-keeping enzymes and has ramifications for the wider all-a NTP pyrophosphohydrolase family.
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On the catalytic mechanism of dimeric dUTPases.,Hemsworth GR, Gonzalez-Pacanowska D, Wilson KS Biochem J. 2013 Sep 4. PMID:24001052<ref>PMID:24001052</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 4dl8" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: DUTP diphosphatase]]
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[[Category: Large Structures]]
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[[Category: Gonzalez-Pacanowska, D]]
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[[Category: Trypanosoma brucei]]
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[[Category: Hemsworth, G R]]
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[[Category: Gonzalez-Pacanowska D]]
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[[Category: Wilson, K S]]
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[[Category: Hemsworth GR]]
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[[Category: All alpha ntp pyrophosphatase]]
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[[Category: Wilson KS]]
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[[Category: All alpha ntp pyrophosphohydrolase]]
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[[Category: Hydrolase]]
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Current revision

Crystal structure of Trypanosoma brucei dUTPase with dUMP, planar [AlF3-OPO3] transition state analogue, Mg2+, and Na+

PDB ID 4dl8

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