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[[Image:2qkl.jpg|left|200px]]


{{Structure
==The crystal structure of fission yeast mRNA decapping enzyme Dcp1-Dcp2 complex==
|PDB= 2qkl |SIZE=350|CAPTION= <scene name='initialview01'>2qkl</scene>, resolution 2.330&Aring;
<StructureSection load='2qkl' size='340' side='right'caption='[[2qkl]], [[Resolution|resolution]] 2.33&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=PB:LEAD+(II)+ION'>PB</scene>
<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>
|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>
</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>
|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])
<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>
|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>
<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>
|RELATEDENTRY=
</table>
|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.rcsb.org/pdb/explore.do?structureId=2qkl RCSB]</span>
== 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 ==
'''The crystal structure of fission yeast mRNA decapping enzyme Dcp1-Dcp2 complex'''
[[Image:Consurf_key_small.gif|200px|right]]
 
Check<jmol>
 
  <jmolCheckbox>
==Overview==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qk/2qkl_consurf.spt"</scriptWhenChecked>
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.
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==About this Structure==
  </jmolCheckbox>
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].  
</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].
 
<div style="clear:both"></div>
==Reference==
== References ==
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]
<references/>
[[Category: M(7)G(5')pppN diphosphatase]]
__TOC__
[[Category: Protein complex]]
</StructureSection>
[[Category: Large Structures]]
[[Category: Schizosaccharomyces pombe]]
[[Category: Schizosaccharomyces pombe]]
[[Category: Chen, N.]]
[[Category: Chen N]]
[[Category: She, M.]]
[[Category: She M]]
[[Category: Song, H.]]
[[Category: Song H]]
[[Category: hydrolase]]
[[Category: protein-protein complex]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:50:24 2008''

Latest revision as of 12:16, 21 February 2024

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

2qkl is a 2 chain structure with sequence from Schizosaccharomyces pombe. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.33Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

  1. ↑ 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

2qkl, resolution 2.33Å

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