2v9x

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(New page: 200px<br /><applet load="2v9x" size="350" color="white" frame="true" align="right" spinBox="true" caption="2v9x, resolution 2.20&Aring;" /> '''E138D VARIANT OF ESC...)
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[[Image:2v9x.gif|left|200px]]<br /><applet load="2v9x" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2v9x, resolution 2.20&Aring;" />
 
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'''E138D VARIANT OF ESCHERICHIA COLI DCTP DEAMINASE IN COMPLEX WITH DUTP'''<br />
 
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==Overview==
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==E138D variant of Escherichia coli dCTP deaminase in complex with dUTP==
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In Escherichia coli and Salmonella typhimurium about 80% of the dUMP used, for dTMP synthesis is derived from deamination of dCTP. The dCTP deaminase, produces dUTP that subsequently is hydrolyzed by dUTPase to dUMP and, diphosphate. The dCTP deaminase is regulated by dTTP that inhibits the, enzyme by binding to the active site and induces an inactive conformation, of the trimeric enzyme. We have analyzed the role of residues previously, suggested to play a role in catalysis. The mutant enzymes R115Q, S111C, S111T and E138D were all purified and analyzed for activity. Only S111T, and E138D displayed detectable activity with a 30- and 140-fold reduction, in kcat, respectively. Furthermore, S111T and E138D both showed altered, dTTP inhibition compared to wild-type enzyme. S111T was almost insensitive, to the presence of dTTP. With the E138D enzyme the dTTP dependent increase, in cooperativity of dCTP saturation was absent, although the dTTP, inhibition itself was still cooperative. Modeling of the active site of, the S111T enzyme indicated that this enzyme is restricted in forming the, inactive dTTP binding conformer due to steric hindrance by the additional, methyl group in threonine. The crystal structure of E138D in complex with, dUTP showed a hydrogen bonding network in the active site similar to, wild-type enzyme. However, changes in the hydrogen bond lengths between, the carboxylate and a catalytic water molecule as well as a slightly, different orientation of the pyrimidine ring of the bound nucleotide may, provide an explanation for the reduced activity.
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<StructureSection load='2v9x' size='340' side='right'caption='[[2v9x]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2v9x]] is a 12 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=2V9X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V9X 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]] 2.2&#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=DUT:DEOXYURIDINE-5-TRIPHOSPHATE'>DUT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=2v9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v9x OCA], [https://pdbe.org/2v9x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v9x RCSB], [https://www.ebi.ac.uk/pdbsum/2v9x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v9x ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DCD_ECOLI DCD_ECOLI]
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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/v9/2v9x_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=2v9x 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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In Escherichia coli and Salmonella typhimurium about 80% of the dUMP used for dTMP synthesis is derived from deamination of dCTP. The dCTP deaminase produces dUTP that subsequently is hydrolyzed by dUTPase to dUMP and diphosphate. The dCTP deaminase is regulated by dTTP that inhibits the enzyme by binding to the active site and induces an inactive conformation of the trimeric enzyme. We have analyzed the role of residues previously suggested to play a role in catalysis. The mutant enzymes R115Q, S111C, S111T and E138D were all purified and analyzed for activity. Only S111T and E138D displayed detectable activity with a 30- and 140-fold reduction in k(cat), respectively. Furthermore, S111T and E138D both showed altered dTTP inhibition compared to wild-type enzyme. S111T was almost insensitive to the presence of dTTP. With the E138D enzyme the dTTP dependent increase in cooperativity of dCTP saturation was absent, although the dTTP inhibition itself was still cooperative. Modeling of the active site of the S111T enzyme indicated that this enzyme is restricted in forming the inactive dTTP binding conformer due to steric hindrance by the additional methyl group in threonine. The crystal structure of E138D in complex with dUTP showed a hydrogen bonding network in the active site similar to wild-type enzyme. However, changes in the hydrogen bond lengths between the carboxylate and a catalytic water molecule as well as a slightly different orientation of the pyrimidine ring of the bound nucleotide may provide an explanation for the reduced activity.
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==About this Structure==
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Mutational analysis of the nucleotide binding site of Escherichia coli dCTP deaminase.,Thymark M, Johansson E, Larsen S, Willemoes M Arch Biochem Biophys. 2008 Feb 1;470(1):20-6. Epub 2007 Oct 30. PMID:17996716<ref>PMID:17996716</ref>
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2V9X 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=SO4:'>SO4</scene> and <scene name='pdbligand=DUT:'>DUT</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/dCTP_deaminase dCTP deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.13 3.5.4.13] Known structural/functional Sites: <scene name='pdbsite=AC1:Dut Binding Site For Chain A'>AC1</scene>, <scene name='pdbsite=AC2:Dut Binding Site For Chain B'>AC2</scene>, <scene name='pdbsite=AC3:Dut Binding Site For Chain C'>AC3</scene>, <scene name='pdbsite=AC4:Dut Binding Site For Chain J'>AC4</scene>, <scene name='pdbsite=AC5:Dut Binding Site For Chain K'>AC5</scene>, <scene name='pdbsite=AC6:Dut Binding Site For Chain L'>AC6</scene>, <scene name='pdbsite=AC7:Dut Binding Site For Chain D'>AC7</scene>, <scene name='pdbsite=AC8:Dut Binding Site For Chain E'>AC8</scene>, <scene name='pdbsite=AC9:Dut Binding Site For Chain F'>AC9</scene>, <scene name='pdbsite=BC1:Dut Binding Site For Chain I'>BC1</scene>, <scene name='pdbsite=BC2:Dut Binding Site For Chain G'>BC2</scene>, <scene name='pdbsite=BC3:Dut Binding Site For Chain H'>BC3</scene>, <scene name='pdbsite=BC4:Mg Binding Site For Chain A'>BC4</scene>, <scene name='pdbsite=BC5:Mg Binding Site For Chain B'>BC5</scene>, <scene name='pdbsite=BC6:Mg Binding Site For Chain C'>BC6</scene>, <scene name='pdbsite=BC7:Mg Binding Site For Chain D'>BC7</scene>, <scene name='pdbsite=BC8:Mg Binding Site For Chain E'>BC8</scene>, <scene name='pdbsite=BC9:Mg Binding Site For Chain F'>BC9</scene>, <scene name='pdbsite=CC1:Mg Binding Site For Chain G'>CC1</scene>, <scene name='pdbsite=CC2:Mg Binding Site For Chain I'>CC2</scene>, <scene name='pdbsite=CC3:Mg Binding Site For Chain J'>CC3</scene>, <scene name='pdbsite=CC4:Mg Binding Site For Chain K'>CC4</scene>, <scene name='pdbsite=CC5:Mg Binding Site For Chain L'>CC5</scene>, <scene name='pdbsite=CC6:So4 Binding Site For Chain C'>CC6</scene>, <scene name='pdbsite=CC7:So4 Binding Site For Chain K'>CC7</scene>, <scene name='pdbsite=CC8:So4 Binding Site For Chain G'>CC8</scene> and <scene name='pdbsite=CC9:So4 Binding Site For Chain D'>CC9</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V9X 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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Mutational analysis of the nucleotide binding site of Escherichia coli dCTP deaminase., Thymark M, Johansson E, Larsen S, Willemoes M, Arch Biochem Biophys. 2007 Oct 30;. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17996716 17996716]
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</div>
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[[Category: Escherichia coli]]
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<div class="pdbe-citations 2v9x" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: dCTP deaminase]]
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[[Category: Johansson, E.]]
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[[Category: Larsen, S.]]
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[[Category: Thymark, M.]]
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[[Category: Willemoes, M.]]
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[[Category: DUT]]
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[[Category: MG]]
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[[Category: SO4]]
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[[Category: dctp deaminase]]
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[[Category: dutpase]]
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[[Category: hydrolase]]
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[[Category: nucleotide metabolism]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 12:11:07 2008''
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==See Also==
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*[[Deaminase 3D structures|Deaminase 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: Johansson E]]
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[[Category: Larsen S]]
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[[Category: Thymark M]]
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[[Category: Willemoes M]]

Current revision

E138D variant of Escherichia coli dCTP deaminase in complex with dUTP

PDB ID 2v9x

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