2qkl

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(New page: 200px {{Structure |PDB= 2qkl |SIZE=350|CAPTION= <scene name='initialview01'>2qkl</scene>, resolution 2.330&Aring; |SITE= |LIGAND= <scene name='pdbligand=PB:LEAD+...)
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[[Image:2qkl.jpg|left|200px]]
 
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{{Structure
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==The crystal structure of fission yeast mRNA decapping enzyme Dcp1-Dcp2 complex==
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|PDB= 2qkl |SIZE=350|CAPTION= <scene name='initialview01'>2qkl</scene>, resolution 2.330&Aring;
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<StructureSection load='2qkl' size='340' side='right'caption='[[2qkl]], [[Resolution|resolution]] 2.33&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=PB:LEAD+(II)+ION'>PB</scene>
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<table><tr><td colspan='2'>[[2qkl]] is a 2 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=2QKL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QKL FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/M(7)G(5')pppN_diphosphatase M(7)G(5')pppN diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.30 3.6.1.30] </span>
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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]] 2.33&#8491;</td></tr>
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|GENE= dcp1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 Schizosaccharomyces pombe]), SPAC19A8.12 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 Schizosaccharomyces pombe])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PB:LEAD+(II)+ION'>PB</scene></td></tr>
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|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam06058 DCP1], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam05026 DCP2]</span>
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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=2qkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qkl OCA], [https://pdbe.org/2qkl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qkl RCSB], [https://www.ebi.ac.uk/pdbsum/2qkl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qkl ProSAT]</span></td></tr>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2qkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qkl OCA], [http://www.ebi.ac.uk/pdbsum/2qkl PDBsum], [http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1kfv JenaLib], [http://www.rcsb.org/pdb/explore.do?structureId=2qkl RCSB]</span>
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</table>
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}}
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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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'''The crystal structure of fission yeast mRNA decapping enzyme Dcp1-Dcp2 complex'''
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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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==Overview==
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<jmolCheckbox>
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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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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qk/2qkl_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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==About this Structure==
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<text>to colour the structure by Evolutionary Conservation</text>
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2QKL is a [[Protein complex]] 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=2QKL OCA].
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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=2qkl ConSurf].
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==Reference==
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<div style="clear:both"></div>
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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:[http://www.ncbi.nlm.nih.gov/pubmed/18280239 18280239]
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== References ==
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[[Category: M(7)G(5')pppN diphosphatase]]
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<references/>
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[[Category: Protein complex]]
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Schizosaccharomyces pombe]]
[[Category: Schizosaccharomyces pombe]]
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[[Category: Chen, N.]]
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[[Category: Chen N]]
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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 Mar 26 09:52:39 2008''
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Current revision

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

PDB ID 2qkl

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