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| | <StructureSection load='5n2v' size='340' side='right'caption='[[5n2v]], [[Resolution|resolution]] 3.10Å' scene=''> | | <StructureSection load='5n2v' size='340' side='right'caption='[[5n2v]], [[Resolution|resolution]] 3.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5n2v]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N2V OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5N2V FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5n2v]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N2V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5N2V FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8NK:7-METHYLGUANOSINE+5-DIPHOSPHATE'>8NK</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1Å</td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5n2v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n2v OCA], [http://pdbe.org/5n2v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n2v RCSB], [http://www.ebi.ac.uk/pdbsum/5n2v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n2v ProSAT]</span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8NK:7-METHYLGUANOSINE+5-DIPHOSPHATE'>8NK</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5n2v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n2v OCA], [https://pdbe.org/5n2v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5n2v RCSB], [https://www.ebi.ac.uk/pdbsum/5n2v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5n2v ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DCP1_SCHPO DCP1_SCHPO]] 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:15671491</ref> [[http://www.uniprot.org/uniprot/DCP2_SCHPO DCP2_SCHPO]] 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:15671491</ref> | + | [https://www.uniprot.org/uniprot/DCP1_SCHPO DCP1_SCHPO] 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:15671491</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Holdermann, I]] | + | [[Category: Schizosaccharomyces pombe]] |
| - | [[Category: Sprangers, R]] | + | [[Category: Holdermann I]] |
| - | [[Category: Rna binding protein]] | + | [[Category: Sprangers R]] |
| Structural highlights
Function
DCP1_SCHPO 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.[1]
Publication Abstract from PubMed
Crystal structures of enzymes are indispensable to understanding their mechanisms on a molecular level. It, however, remains challenging to determine which structures are adopted in solution, especially for dynamic complexes. Here, we study the bilobed decapping enzyme Dcp2 that removes the 5' cap structure from eukaryotic mRNA and thereby efficiently terminates gene expression. The numerous Dcp2 structures can be grouped into six states where the domain orientation between the catalytic and regulatory domains significantly differs. Despite this wealth of structural information it is not possible to correlate these states with the catalytic cycle or the activity of the enzyme. Using methyl transverse relaxation-optimized NMR spectroscopy, we demonstrate that only three of the six domain orientations are present in solution, where Dcp2 adopts an open, a closed, or a catalytically active state. We show how mRNA substrate and the activator proteins Dcp1 and Edc1 influence the dynamic equilibria between these states and how this modulates catalytic activity. Importantly, the active state of the complex is only stably formed in the presence of both activators and the mRNA substrate or the m7GDP decapping product, which we rationalize based on a crystal structure of the Dcp1:Dcp2:Edc1:m7GDP complex. Interestingly, we find that the activating mechanisms in Dcp2 also result in a shift of the substrate specificity from bacterial to eukaryotic mRNA.
Changes in conformational equilibria regulate the activity of the Dcp2 decapping enzyme.,Wurm JP, Holdermann I, Overbeck JH, Mayer PHO, Sprangers R Proc Natl Acad Sci U S A. 2017 Jun 6;114(23):6034-6039. doi:, 10.1073/pnas.1704496114. Epub 2017 May 22. PMID:28533364[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Sakuno T, Araki Y, Ohya Y, Kofuji S, Takahashi S, Hoshino S, Katada T. Decapping reaction of mRNA requires Dcp1 in fission yeast: its characterization in different species from yeast to human. J Biochem. 2004 Dec;136(6):805-12. PMID:15671491 doi:http://dx.doi.org/136/6/805
- ↑ Wurm JP, Holdermann I, Overbeck JH, Mayer PHO, Sprangers R. Changes in conformational equilibria regulate the activity of the Dcp2 decapping enzyme. Proc Natl Acad Sci U S A. 2017 Jun 6;114(23):6034-6039. doi:, 10.1073/pnas.1704496114. Epub 2017 May 22. PMID:28533364 doi:http://dx.doi.org/10.1073/pnas.1704496114
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