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| | ==Crystal structure of S. pombe Dcp2:Dcp1:Edc1 mRNA decapping complex== | | ==Crystal structure of S. pombe Dcp2:Dcp1:Edc1 mRNA decapping complex== |
| - | <StructureSection load='5j3t' size='340' side='right' caption='[[5j3t]], [[Resolution|resolution]] 1.60Å' scene=''> | + | <StructureSection load='5j3t' size='340' side='right'caption='[[5j3t]], [[Resolution|resolution]] 1.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5j3t]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J3T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J3T FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5j3t]] is a 3 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=5J3T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J3T FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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]] 1.6Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5j3q|5j3q]], [[5j3y|5j3y]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5'-(N(7)-methylguanosine_5'-triphospho)-[mRNA]_hydrolase 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.62 3.6.1.62] </span></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=5j3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j3t OCA], [https://pdbe.org/5j3t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j3t RCSB], [https://www.ebi.ac.uk/pdbsum/5j3t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j3t ProSAT]</span></td></tr> |
| - | <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=5j3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j3t OCA], [http://pdbe.org/5j3t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j3t RCSB], [http://www.ebi.ac.uk/pdbsum/5j3t PDBsum]</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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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Chang, C T]] | + | [[Category: Large Structures]] |
| - | [[Category: Izaurralde, E]] | + | [[Category: Schizosaccharomyces pombe]] |
| - | [[Category: Jonas, S]] | + | [[Category: Chang CT]] |
| - | [[Category: Muthukumar, S]] | + | [[Category: Izaurralde E]] |
| - | [[Category: Valkov, E]]
| + | [[Category: Jonas S]] |
| - | [[Category: Weichenrieder, O]] | + | [[Category: Muthukumar S]] |
| - | [[Category: Decapping]] | + | [[Category: Valkov E]] |
| - | [[Category: Evh1]] | + | [[Category: Weichenrieder O]] |
| - | [[Category: Hydrolase]] | + | |
| - | [[Category: Mrna decay]]
| + | |
| - | [[Category: Nudix]]
| + | |
| 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
The removal of the mRNA 5' cap (decapping) by Dcp2 shuts down translation and commits mRNA to full degradation. Dcp2 activity is enhanced by activator proteins such as Dcp1 and Edc1. However, owing to conformational flexibility, the active conformation of Dcp2 and the mechanism of decapping activation have remained unknown. Here, we report a 1.6-A-resolution crystal structure of the Schizosaccharomyces pombe Dcp2-Dcp1 heterodimer in an unprecedented conformation that is tied together by an intrinsically disordered peptide from Edc1. In this ternary complex, an unforeseen rotation of the Dcp2 catalytic domain allows residues from both Dcp2 and Dcp1 to cooperate in RNA binding, thus explaining decapping activation by increased substrate affinity. The architecture of the Dcp2-Dcp1-Edc1 complex provides a rationale for the conservation of a sequence motif in Edc1 that is also present in unrelated decapping activators, thus indicating that the presently described mechanism of decapping activation is evolutionarily conserved.
Structure of the Dcp2-Dcp1 mRNA-decapping complex in the activated conformation.,Valkov E, Muthukumar S, Chang CT, Jonas S, Weichenrieder O, Izaurralde E Nat Struct Mol Biol. 2016 May 16. doi: 10.1038/nsmb.3232. PMID:27183195[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
- ↑ Valkov E, Muthukumar S, Chang CT, Jonas S, Weichenrieder O, Izaurralde E. Structure of the Dcp2-Dcp1 mRNA-decapping complex in the activated conformation. Nat Struct Mol Biol. 2016 May 16. doi: 10.1038/nsmb.3232. PMID:27183195 doi:http://dx.doi.org/10.1038/nsmb.3232
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