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2py4

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(New page: 200px<br /><applet load="2py4" size="450" color="white" frame="true" align="right" spinBox="true" caption="2py4, resolution 1.49&Aring;" /> '''Full length structur...)
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[[Image:2py4.gif|left|200px]]<br /><applet load="2py4" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2py4, resolution 1.49&Aring;" />
 
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'''Full length structure of the Mycobacterium tuberculosis dUTPase complexed with magnesium and alpha,beta-imido-dUTP.'''<br />
 
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==About this Structure==
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==Full length structure of the Mycobacterium tuberculosis dUTPase complexed with magnesium and alpha,beta-imido-dUTP.==
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2PY4 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis] with MG, DUP and TRS as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2PY4 OCA].
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<StructureSection load='2py4' size='340' side='right'caption='[[2py4]], [[Resolution|resolution]] 1.49&Aring;' scene=''>
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[[Category: Mycobacterium tuberculosis]]
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== Structural highlights ==
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[[Category: Single protein]]
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<table><tr><td colspan='2'>[[2py4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PY4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PY4 FirstGlance]. <br>
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[[Category: dUTP diphosphatase]]
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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]] 1.49&#8491;</td></tr>
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[[Category: Barabas, O.]]
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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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[[Category: Nagy, N.]]
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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=2py4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2py4 OCA], [https://pdbe.org/2py4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2py4 RCSB], [https://www.ebi.ac.uk/pdbsum/2py4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2py4 ProSAT]</span></td></tr>
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[[Category: Takacs, E.]]
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</table>
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[[Category: Vertessy, G.B.]]
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== Function ==
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[[Category: DUP]]
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[https://www.uniprot.org/uniprot/DUT_MYCTU DUT_MYCTU] 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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[[Category: MG]]
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== Evolutionary Conservation ==
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[[Category: TRS]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: enzyme-ligand complex]]
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Check<jmol>
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[[Category: jelly-roll]]
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/py/2py4_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=2py4 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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dUTPases are essential to eliminate dUTP for DNA integrity and provide dUMP for thymidylate biosynthesis. Mycobacterium tuberculosis apparently lacks any other thymidylate biosynthesis pathway, therefore dUTPase is a promising antituberculotic drug target. Crystal structure of the mycobacterial enzyme in complex with the isosteric substrate analog, alpha,beta-imido-dUTP and Mg(2+) at 1.5A resolution was determined that visualizes the full-length C-terminus, previously not localized. Interactions of a conserved motif important in catalysis, the Mycobacterium-specific five-residue-loop insert and C-terminal tetrapeptide could now be described in detail. Stacking of C-terminal histidine upon the uracil moiety prompted replacement with tryptophan. The resulting sensitive fluorescent sensor enables fast screening for binding of potential inhibitors to the active site. K(d) for alpha,beta-imido-dUTP binding to mycobacterial dUTPase is determined to be 10-fold less than for human dUTPase, which is to be considered in drug optimization. A robust continuous activity assay for kinetic screening is proposed.
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 13:43:57 2007''
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Active site of mycobacterial dUTPase: structural characteristics and a built-in sensor.,Varga B, Barabas O, Takacs E, Nagy N, Nagy P, Vertessy BG Biochem Biophys Res Commun. 2008 Aug 15;373(1):8-13. Epub 2008 Jun 2. PMID:18519027<ref>PMID:18519027</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 2py4" style="background-color:#fffaf0;"></div>
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==See Also==
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*[[DUTPase 3D structures|DUTPase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Mycobacterium tuberculosis]]
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[[Category: Barabas O]]
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[[Category: Nagy N]]
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[[Category: Takacs E]]
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[[Category: Vertessy BG]]

Current revision

Full length structure of the Mycobacterium tuberculosis dUTPase complexed with magnesium and alpha,beta-imido-dUTP.

PDB ID 2py4

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