1rnj

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[[Image:1rnj.gif|left|200px]]<br /><applet load="1rnj" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1rnj, resolution 1.70&Aring;" />
 
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'''Crystal structure of inactive mutant dUTPase complexed with substrate analogue imido-dUTP'''<br />
 
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==Overview==
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==Crystal structure of inactive mutant dUTPase complexed with substrate analogue imido-dUTP==
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<StructureSection load='1rnj' size='340' side='right'caption='[[1rnj]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1rnj]] 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=1RNJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RNJ 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]] 1.7&#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=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=1rnj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rnj OCA], [https://pdbe.org/1rnj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rnj RCSB], [https://www.ebi.ac.uk/pdbsum/1rnj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rnj 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/1rnj_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=1rnj 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 ==
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.
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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==About this Structure==
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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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1RNJ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=DUP:'>DUP</scene> and <scene name='pdbligand=TRS:'>TRS</scene> 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1RNJ OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15208312 15208312]
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</div>
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[[Category: Escherichia coli]]
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<div class="pdbe-citations 1rnj" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: dUTP diphosphatase]]
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[[Category: Barabas, O.]]
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[[Category: Kovari, J.]]
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[[Category: Pongracz, V.]]
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[[Category: Vertessy, B G.]]
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[[Category: Wilmanns, M.]]
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[[Category: DUP]]
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[[Category: MG]]
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[[Category: TRS]]
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[[Category: enzyme-ligand complex]]
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[[Category: jelly roll]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:52:41 2008''
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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: Escherichia coli]]
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[[Category: Large Structures]]
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[[Category: Barabas O]]
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[[Category: Kovari J]]
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[[Category: Pongracz V]]
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[[Category: Vertessy BG]]
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[[Category: Wilmanns M]]

Current revision

Crystal structure of inactive mutant dUTPase complexed with substrate analogue imido-dUTP

PDB ID 1rnj

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