2vgn

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{{Seed}}
 
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[[Image:2vgn.png|left|200px]]
 
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==Structure of S. cerevisiae Dom34, a translation termination-like factor involved in RNA quality control pathways and interacting with Hbs1 (SelenoMet-labeled protein)==
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The line below this paragraph, containing "STRUCTURE_2vgn", creates the "Structure Box" on the page.
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<StructureSection load='2vgn' size='340' side='right'caption='[[2vgn]], [[Resolution|resolution]] 2.50&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'>[[2vgn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VGN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VGN FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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{{STRUCTURE_2vgn| PDB=2vgn | SCENE= }}
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2vgm|2vgm]]</div></td></tr>
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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=2vgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vgn OCA], [https://pdbe.org/2vgn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vgn RCSB], [https://www.ebi.ac.uk/pdbsum/2vgn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vgn ProSAT]</span></td></tr>
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</table>
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== Function ==
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[[https://www.uniprot.org/uniprot/DOM34_YEAST DOM34_YEAST]] Involved in protein translation. Together with HBS1, may function in recognizing stalled ribosomes and triggering endonucleolytic cleavage of the mRNA, a mechanism to release non-functional ribosomes and degrade damaged mRNAs. The complex formed by DOM34 and HBS1 has ribonuclease activity towards double-stranded RNA substrates, but does not cleave single-stranded RNA. Acts as endonuclease; has no exonuclease activity. Increases the affinity of HBS1 for GTP, but nor for GDP. Promotes G1 progression and differentiation and is involved in mitotic and meiotic cell divisions.<ref>PMID:16554824</ref> <ref>PMID:17889667</ref> <ref>PMID:18180287</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/vg/2vgn_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=2vgn 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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The yeast protein Dom34 has been described to play a critical role in a newly identified mRNA decay pathway called No-Go decay. This pathway clears cells from mRNAs inducing translational stalls through endonucleolytic cleavage. Dom34 is related to the translation termination factor eRF1 and physically interacts with Hbs1, which is itself related to eRF3. We have solved the 2.5-A resolution crystal structure of Saccharomyces cerevisiae Dom34. This protein is organized in three domains with the central and C-terminal domains structurally homologous to those from eRF1. The N-terminal domain of Dom34 is different from eRF1. It adopts a Sm-fold that is often involved in the recognition of mRNA stem loops or in the recruitment of mRNA degradation machinery. The comparison of eRF1 and Dom34 domains proposed to interact directly with eRF3 and Hbs1, respectively, highlights striking structural similarities with eRF1 motifs identified to be crucial for the binding to eRF3. In addition, as observed for eRF1 that enhances eRF3 binding to GTP, the interaction of Dom34 with Hbs1 results in an increase in the affinity constant of Hbs1 for GTP but not GDP. Taken together, these results emphasize that eukaryotic cells have evolved two structurally related complexes able to interact with ribosomes either paused at a stop codon or stalled in translation by the presence of a stable stem loop and to trigger ribosome release by catalyzing chemical bond hydrolysis.
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===STRUCTURE OF YEAST DOM34 : A PROTEIN RELATED TO TRANSLATION TERMINATION FACTOR ERF1 AND INVOLVED IN NO-GO DECAY.===
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Structure of yeast Dom34: a protein related to translation termination factor Erf1 and involved in No-Go decay.,Graille M, Chaillet M, van Tilbeurgh H J Biol Chem. 2008 Mar 14;283(11):7145-54. Epub 2008 Jan 7. PMID:18180287<ref>PMID:18180287</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_18180287}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2vgn" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 18180287 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_18180287}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Baker's yeast]]
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2VGN is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VGN OCA].
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[[Category: Large Structures]]
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[[Category: Chaillet, M]]
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==Reference==
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[[Category: Graille, M]]
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<ref group="xtra">PMID:18180287</ref><references group="xtra"/>
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[[Category: Tilbeurgh, H Van]]
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[[Category: Saccharomyces cerevisiae]]
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[[Category: Chaillet, M.]]
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[[Category: Graille, M.]]
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[[Category: Tilbeurgh, H Van.]]
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[[Category: Cell cycle]]
[[Category: Cell cycle]]
[[Category: Cell division]]
[[Category: Cell division]]
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[[Category: Translation regulation]]
[[Category: Translation regulation]]
[[Category: Translation termination factor]]
[[Category: Translation termination factor]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 14:20:30 2009''
 

Current revision

Structure of S. cerevisiae Dom34, a translation termination-like factor involved in RNA quality control pathways and interacting with Hbs1 (SelenoMet-labeled protein)

PDB ID 2vgn

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