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4kg3

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==Crystal structure of Saccharomyces cerevisiae Dcp2 Nudix domain in complex with Mg (E153Q mutation)==
==Crystal structure of Saccharomyces cerevisiae Dcp2 Nudix domain in complex with Mg (E153Q mutation)==
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<StructureSection load='4kg3' size='340' side='right' caption='[[4kg3]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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<StructureSection load='4kg3' size='340' side='right'caption='[[4kg3]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4kg3]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KG3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KG3 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4kg3]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KG3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KG3 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=MG:MAGNESIUM+ION'>MG</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]] 1.7&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4k6e|4k6e]], [[4kg4|4kg4]]</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=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DCP2, N1917, PSU1, YNL118C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=4kg3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kg3 OCA], [https://pdbe.org/4kg3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kg3 RCSB], [https://www.ebi.ac.uk/pdbsum/4kg3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kg3 ProSAT]</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=4kg3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kg3 OCA], [http://pdbe.org/4kg3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4kg3 RCSB], [http://www.ebi.ac.uk/pdbsum/4kg3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4kg3 ProSAT]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/DCP2_YEAST DCP2_YEAST]] Catalytic component of the decapping complex necessary for the degradation of mRNAs, both in normal mRNA turnover and in nonsense-mediated mRNA decay. Removes the 7-methyl guanine cap structure from mRNA molecules, yielding a 5'-phosphorylated mRNA fragment and 7m-GDP. Decapping is the major pathway of mRNA degradation in yeast. It occurs through deadenylation, decapping and subsequent 5' to 3' exonucleolytic decay of the transcript body.<ref>PMID:10508173</ref> <ref>PMID:11139489</ref> <ref>PMID:11741542</ref> <ref>PMID:12554866</ref>
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[https://www.uniprot.org/uniprot/DCP2_YEAST DCP2_YEAST] Catalytic component of the decapping complex necessary for the degradation of mRNAs, both in normal mRNA turnover and in nonsense-mediated mRNA decay. Removes the 7-methyl guanine cap structure from mRNA molecules, yielding a 5'-phosphorylated mRNA fragment and 7m-GDP. Decapping is the major pathway of mRNA degradation in yeast. It occurs through deadenylation, decapping and subsequent 5' to 3' exonucleolytic decay of the transcript body.<ref>PMID:10508173</ref> <ref>PMID:11139489</ref> <ref>PMID:11741542</ref> <ref>PMID:12554866</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Removal of the 5' cap structure by Dcp2 is a major step in several 5'-3' mRNA decay pathways. The activity of Dcp2 is enhanced by Dcp1 and bound coactivators, yet the details of how these interactions are linked to chemistry are poorly understood. Here, we report three crystal structures of the catalytic Nudix hydrolase domain of Dcp2 that demonstrate binding of a catalytically essential metal ion, and enzyme kinetics are used to identify several key active site residues involved in acid/base chemistry of decapping. Using nuclear magnetic resonance and molecular dynamics, we find that a conserved metal binding loop on the catalytic domain undergoes conformational changes during the catalytic cycle. These findings describe key events during the chemical step of decapping, suggest local active site conformational changes are important for activity, and provide a framework to explain stimulation of catalysis by the regulatory domain of Dcp2 and associated coactivators.
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Active Site Conformational Dynamics Are Coupled to Catalysis in the mRNA Decapping Enzyme Dcp2.,Aglietti RA, Floor SN, McClendon CL, Jacobson MP, Gross JD Structure. 2013 Jul 31. pii: S0969-2126(13)00245-1. doi:, 10.1016/j.str.2013.06.021. PMID:23911090<ref>PMID:23911090</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 4kg3" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Baker's yeast]]
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[[Category: Large Structures]]
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[[Category: Aglietti, R A]]
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[[Category: Saccharomyces cerevisiae S288C]]
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[[Category: Floor, S N]]
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[[Category: Aglietti RA]]
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[[Category: Gross, J D]]
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[[Category: Floor SN]]
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[[Category: Hydrolase]]
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[[Category: Gross JD]]
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[[Category: Mrna decapping]]
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[[Category: Mrna decay]]
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[[Category: Nudix]]
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Current revision

Crystal structure of Saccharomyces cerevisiae Dcp2 Nudix domain in complex with Mg (E153Q mutation)

PDB ID 4kg3

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