2qkm

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{{Seed}}
 
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[[Image:2qkm.png|left|200px]]
 
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==The crystal structure of fission yeast mRNA decapping enzyme Dcp1-Dcp2 complex==
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The line below this paragraph, containing "STRUCTURE_2qkm", creates the "Structure Box" on the page.
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<StructureSection load='2qkm' size='340' side='right'caption='[[2qkm]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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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]] 2.8&#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=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene></td></tr>
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{{STRUCTURE_2qkm| PDB=2qkm | SCENE= }}
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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=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>
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</table>
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== Function ==
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[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>
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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/qk/2qkm_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=2qkm 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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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.
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===The crystal structure of fission yeast mRNA decapping enzyme Dcp1-Dcp2 complex===
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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>
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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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The line below this paragraph, {{ABSTRACT_PUBMED_18280239}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2qkm" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 18280239 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_18280239}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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2QKM is a 8 chains structure of sequences from [http://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QKM OCA].
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[[Category: Messenger RNA Capping]]
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[[Category: RCSB PDB Molecule of the Month]]
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==Reference==
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<ref group="xtra">PMID:18280239</ref><references group="xtra"/>
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[[Category: Schizosaccharomyces pombe]]
[[Category: Schizosaccharomyces pombe]]
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[[Category: She, M.]]
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[[Category: She M]]
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[[Category: Song, H.]]
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[[Category: Song H]]
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[[Category: Hydrolase]]
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[[Category: Protein-protein complex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 06:33:58 2009''
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Current revision

The crystal structure of fission yeast mRNA decapping enzyme Dcp1-Dcp2 complex

PDB ID 2qkm

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