2vgm

From Proteopedia

(Difference between revisions)

Current revision

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

Structural highlights

2vgm is a 1 chain structure with sequence from Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.6Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1] ^[2] ^[3]

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 PubMed

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.

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^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Doma MK, Parker R. Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation. Nature. 2006 Mar 23;440(7083):561-4. PMID:16554824 doi:nature04530
↑ Lee HH, Kim YS, Kim KH, Heo I, Kim SK, Kim O, Kim HK, Yoon JY, Kim HS, Kim do J, Lee SJ, Yoon HJ, Kim SJ, Lee BG, Song HK, Kim VN, Park CM, Suh SW. Structural and functional insights into Dom34, a key component of no-go mRNA decay. Mol Cell. 2007 Sep 21;27(6):938-50. PMID:17889667 doi:10.1016/j.molcel.2007.07.019
↑ Graille M, Chaillet M, van Tilbeurgh H. Structure of yeast Dom34: a protein related to translation termination factor Erf1 and involved in No-Go decay. J Biol Chem. 2008 Mar 14;283(11):7145-54. Epub 2008 Jan 7. PMID:18180287 doi:10.1074/jbc.M708224200
↑ Graille M, Chaillet M, van Tilbeurgh H. Structure of yeast Dom34: a protein related to translation termination factor Erf1 and involved in No-Go decay. J Biol Chem. 2008 Mar 14;283(11):7145-54. Epub 2008 Jan 7. PMID:18180287 doi:10.1074/jbc.M708224200

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2vgm"

Categories: Large Structures | Saccharomyces cerevisiae S288C | Chaillet M | Graille M | Van Tilbeurgh H

@@ Line 1: / Line 1: @@
-==STRUCTURE OF YEAST DOM34 : A PROTEIN RELATED TO TRANSLATION TERMINATION FACTOR ERF1 AND INVOLVED IN NO-GO DECAY.==
-<StructureSection load='2vgm' size='340' side='right' caption='[[2vgm]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+==Structure of S. cerevisiae Dom34, a translation termination-like factor involved in RNA quality control pathways and interacting with Hbs1 (Unlabeled protein)==
+<StructureSection load='2vgm' size='340' side='right'caption='[[2vgm]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2vgm]] is a 1 chain structure with sequence 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=2VGM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VGM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2vgm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VGM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VGM FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2vgn|2vgn]]</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2vgm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vgm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vgm RCSB], [http://www.ebi.ac.uk/pdbsum/2vgm PDBsum]</span></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=2vgm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vgm OCA], [https://pdbe.org/2vgm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vgm RCSB], [https://www.ebi.ac.uk/pdbsum/2vgm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vgm ProSAT]</span></td></tr>
-<table>
+</table>
+== Function ==
+[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>
 == 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/vg/2vgm_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vg/2vgm_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2vgm ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 24: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2vgm" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Saccharomyces cerevisiae]]
+[[Category: Large Structures]]
-[[Category: Chaillet, M.]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Graille, M.]]
+[[Category: Chaillet M]]
-[[Category: Tilbeurgh, H Van.]]
+[[Category: Graille M]]
-[[Category: Cell cycle]]
+[[Category: Van Tilbeurgh H]]
-[[Category: Cell division]]
-[[Category: Meiosis]]
-[[Category: Mitosis]]
-[[Category: Mrna degradation]]
-[[Category: No-go decay]]
-[[Category: Nucleotide binding]]
-[[Category: Protein biosynthesis]]
-[[Category: Translation regulation]]
-[[Category: Translation termination factor]]

2vgm

From Proteopedia

Current revision

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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