1rn8

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[[Image:1rn8.png|left|200px]]
 
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{{STRUCTURE_1rn8| PDB=1rn8 | SCENE= }}
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==Crystal structure of dUTPase complexed with substrate analogue imido-dUTP==
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<StructureSection load='1rn8' size='340' side='right'caption='[[1rn8]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1rn8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RN8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RN8 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]] 1.93&#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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DUP:2-DEOXYURIDINE+5-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=1rn8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rn8 OCA], [https://pdbe.org/1rn8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rn8 RCSB], [https://www.ebi.ac.uk/pdbsum/1rn8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rn8 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DUT_ECOLI DUT_ECOLI] This enzyme is involved in nucleotide metabolism: it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP so that uracil cannot be incorporated into DNA.[HAMAP-Rule:MF_00116]
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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/rn/1rn8_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=1rn8 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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dUTPase is essential to keep uracil out of DNA. Crystal structures of substrate (dUTP and alpha,beta-imino-dUTP) and product complexes of wild type and mutant dUTPases were determined to reveal how an enzyme responsible for DNA integrity functions. A kinetic analysis of wild type and mutant dUTPases was performed to obtain relevant mechanistic information in solution. Substrate hydrolysis is shown to be initiated via in-line nucleophile attack of a water molecule oriented by an activating conserved aspartate residue. Substrate binding in a catalytically competent conformation is achieved by (i) multiple interactions of the triphosphate moiety with catalysis-assisting Mg2+, (ii) a concerted motion of residues from three conserved enzyme motifs as compared with the apoenzyme, and (iii) an intricate hydrogen-bonding network that includes several water molecules in the active site. Results provide an understanding for the catalytic role of conserved residues in dUTPases.
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===Crystal structure of dUTPase complexed with substrate analogue imido-dUTP===
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Structural insights into the catalytic mechanism of phosphate ester hydrolysis by dUTPase.,Barabas O, Pongracz V, Kovari J, Wilmanns M, Vertessy BG J Biol Chem. 2004 Oct 8;279(41):42907-15. Epub 2004 Jun 17. PMID:15208312<ref>PMID:15208312</ref>
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{{ABSTRACT_PUBMED_15208312}}
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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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==About this Structure==
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<div class="pdbe-citations 1rn8" style="background-color:#fffaf0;"></div>
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[[1rn8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RN8 OCA].
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==See Also==
==See Also==
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*[[Deoxyuridine 5'-triphosphate nucleotidohydrolase|Deoxyuridine 5'-triphosphate nucleotidohydrolase]]
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*[[DUTPase 3D structures|DUTPase 3D structures]]
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== References ==
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==Reference==
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<references/>
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<ref group="xtra">PMID:015208312</ref><references group="xtra"/>
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__TOC__
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</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: DUTP diphosphatase]]
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[[Category: Large Structures]]
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[[Category: Barabas, O.]]
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[[Category: Barabas O]]
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[[Category: Kovari, J.]]
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[[Category: Kovari J]]
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[[Category: Pongracz, V.]]
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[[Category: Pongracz V]]
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[[Category: Vertessy, B G.]]
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[[Category: Vertessy BG]]
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[[Category: Wilmanns, M.]]
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[[Category: Wilmanns M]]
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[[Category: Enzyme-ligand complex]]
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[[Category: Hydrolase]]
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[[Category: Jelly roll]]
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Current revision

Crystal structure of dUTPase complexed with substrate analogue imido-dUTP

PDB ID 1rn8

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