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< | ==The crystal structure of fission yeast mRNA decapping enzyme Dcp1-Dcp2 complex== | ||
<StructureSection load='2qkm' size='340' side='right'caption='[[2qkm]], [[Resolution|resolution]] 2.80Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2qkm]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. The January 2012 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Messenger RNA Capping'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2012_1 10.2210/rcsb_pdb/mom_2012_1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QKM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QKM FirstGlance]. <br> | |||
or | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</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=2qkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qkm OCA], [https://pdbe.org/2qkm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qkm RCSB], [https://www.ebi.ac.uk/pdbsum/2qkm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qkm ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[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> | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qk/2qkm_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</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=2qkm ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
A critical step in mRNA degradation is the removal of the 5' cap structure, which is catalyzed by the Dcp1-Dcp2 complex. The crystal structure of an S. pombe Dcp1p-Dcp2n complex combined with small-angle X-ray scattering analysis (SAXS) reveals that Dcp2p exists in open and closed conformations, with the closed complex being, or closely resembling, the catalytically more active form. This suggests that a conformational change between these open and closed complexes might control decapping. A bipartite RNA-binding channel containing the catalytic site and Box B motif is identified with a bound ATP located in the catalytic pocket in the closed complex, suggesting possible interactions that facilitate substrate binding. Dcp1 stimulates the activity of Dcp2 by promoting and/or stabilizing the closed complex. Notably, the interface of Dcp1 and Dcp2 is not fully conserved, explaining why the Dcp1-Dcp2 interaction in higher eukaryotes requires an additional factor. | |||
Structural basis of dcp2 recognition and activation by dcp1.,She M, Decker CJ, Svergun DI, Round A, Chen N, Muhlrad D, Parker R, Song H Mol Cell. 2008 Feb 15;29(3):337-49. PMID:18280239<ref>PMID:18280239</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2qkm" style="background-color:#fffaf0;"></div> | |||
== References == | |||
--> | <references/> | ||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Large Structures]] | ||
[[Category: Messenger RNA Capping]] | |||
[[Category: RCSB PDB Molecule of the Month]] | |||
[[Category: | |||
[[Category: Schizosaccharomyces pombe]] | [[Category: Schizosaccharomyces pombe]] | ||
[[Category: She | [[Category: She M]] | ||
[[Category: Song | [[Category: Song H]] | ||
Latest revision as of 14:35, 30 August 2023
The crystal structure of fission yeast mRNA decapping enzyme Dcp1-Dcp2 complexThe crystal structure of fission yeast mRNA decapping enzyme Dcp1-Dcp2 complex
Structural highlights
FunctionDCP1_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] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedA critical step in mRNA degradation is the removal of the 5' cap structure, which is catalyzed by the Dcp1-Dcp2 complex. The crystal structure of an S. pombe Dcp1p-Dcp2n complex combined with small-angle X-ray scattering analysis (SAXS) reveals that Dcp2p exists in open and closed conformations, with the closed complex being, or closely resembling, the catalytically more active form. This suggests that a conformational change between these open and closed complexes might control decapping. A bipartite RNA-binding channel containing the catalytic site and Box B motif is identified with a bound ATP located in the catalytic pocket in the closed complex, suggesting possible interactions that facilitate substrate binding. Dcp1 stimulates the activity of Dcp2 by promoting and/or stabilizing the closed complex. Notably, the interface of Dcp1 and Dcp2 is not fully conserved, explaining why the Dcp1-Dcp2 interaction in higher eukaryotes requires an additional factor. Structural basis of dcp2 recognition and activation by dcp1.,She M, Decker CJ, Svergun DI, Round A, Chen N, Muhlrad D, Parker R, Song H Mol Cell. 2008 Feb 15;29(3):337-49. PMID:18280239[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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