2pmd
From Proteopedia
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| - | [[Image:2pmd.jpg|left|200px]] | ||
| - | + | ==The structures of aIF2gamma subunit from the archaeon Sulfolobus solfataricus in the GDP-bound form.== | |
| - | + | <StructureSection load='2pmd' size='340' side='right'caption='[[2pmd]], [[Resolution|resolution]] 2.65Å' scene=''> | |
| - | + | == Structural highlights == | |
| - | + | <table><tr><td colspan='2'>[[2pmd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus Saccharolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PMD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PMD FirstGlance]. <br> | |
| - | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.65Å</td></tr> | |
| - | --> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</scene></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=2pmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pmd OCA], [https://pdbe.org/2pmd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pmd RCSB], [https://www.ebi.ac.uk/pdbsum/2pmd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pmd ProSAT]</span></td></tr> | |
| - | + | </table> | |
| - | + | == Function == | |
| - | + | [https://www.uniprot.org/uniprot/IF2G_SACS2 IF2G_SACS2] eIF-2 functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA.[HAMAP-Rule:MF_00119] | |
| - | + | == 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/pm/2pmd_consurf.spt"</scriptWhenChecked> | ||
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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/main_output.php?pdb_ID=2pmd ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
Heterotrimeric a/eIF2alphabetagamma (archaeal homologue of the eukaryotic translation initiation factor 2 with alpha, beta and gamma subunits) delivers charged initiator tRNA (tRNAi) to the small ribosomal subunit. In this work, we determined the structures of aIF2gamma from the archaeon Sulfolobus solfataricus in the nucleotide-free and GDP-bound forms. Comparison of the free, GDP and Gpp(NH)p-Mg2+ forms of aIF2gamma revealed a sequence of conformational changes upon GDP and GTP binding. Our results show that the affinity of GDP to the G domain of the gamma subunit is higher than that of Gpp(NH)p. In analyzing a pyrophosphate molecule binding to domain II of the gamma subunit, we found a cleft that is very suitable for the acceptor stem of tRNA accommodation. It allows the suggestion of an alternative position for Met-tRNA i Met on the alphagamma intersubunit dimer, at variance with a recently published one. In the model reported here, the acceptor stem of the tRNAi is approximately perpendicular to that of tRNA in the ternary complex elongation factor Tu-Gpp(NH)p-tRNA. According to our analysis, the elbow and T stem of Met-tRNA i Met in this position should make extensive contact with the alpha subunit of aIF2. Thus, this model is in good agreement with experimental data showing that the alpha subunit of aIF2 is necessary for the stable interaction of aIF2gamma with Met-tRNA i Met. | Heterotrimeric a/eIF2alphabetagamma (archaeal homologue of the eukaryotic translation initiation factor 2 with alpha, beta and gamma subunits) delivers charged initiator tRNA (tRNAi) to the small ribosomal subunit. In this work, we determined the structures of aIF2gamma from the archaeon Sulfolobus solfataricus in the nucleotide-free and GDP-bound forms. Comparison of the free, GDP and Gpp(NH)p-Mg2+ forms of aIF2gamma revealed a sequence of conformational changes upon GDP and GTP binding. Our results show that the affinity of GDP to the G domain of the gamma subunit is higher than that of Gpp(NH)p. In analyzing a pyrophosphate molecule binding to domain II of the gamma subunit, we found a cleft that is very suitable for the acceptor stem of tRNA accommodation. It allows the suggestion of an alternative position for Met-tRNA i Met on the alphagamma intersubunit dimer, at variance with a recently published one. In the model reported here, the acceptor stem of the tRNAi is approximately perpendicular to that of tRNA in the ternary complex elongation factor Tu-Gpp(NH)p-tRNA. According to our analysis, the elbow and T stem of Met-tRNA i Met in this position should make extensive contact with the alpha subunit of aIF2. Thus, this model is in good agreement with experimental data showing that the alpha subunit of aIF2 is necessary for the stable interaction of aIF2gamma with Met-tRNA i Met. | ||
| - | + | New insights into the interactions of the translation initiation factor 2 from archaea with guanine nucleotides and initiator tRNA.,Nikonov O, Stolboushkina E, Nikulin A, Hasenohrl D, Blasi U, Manstein DJ, Fedorov R, Garber M, Nikonov S J Mol Biol. 2007 Oct 19;373(2):328-36. Epub 2007 Aug 2. PMID:17825838<ref>PMID:17825838</ref> | |
| - | + | ||
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | [[Category: | + | <div class="pdbe-citations 2pmd" style="background-color:#fffaf0;"></div> |
| - | [[Category: | + | == References == |
| - | [[Category: Blaesi | + | <references/> |
| - | [[Category: Fedorov | + | __TOC__ |
| - | [[Category: Garber | + | </StructureSection> |
| - | [[Category: Hasenohrl | + | [[Category: Large Structures]] |
| - | [[Category: Manstein | + | [[Category: Saccharolobus solfataricus]] |
| - | [[Category: Nikonov | + | [[Category: Blaesi U]] |
| - | [[Category: Nikonov | + | [[Category: Fedorov RV]] |
| - | [[Category: Nikulin | + | [[Category: Garber MB]] |
| - | [[Category: Stolboushkina | + | [[Category: Hasenohrl D]] |
| - | + | [[Category: Manstein DJ]] | |
| - | + | [[Category: Nikonov OS]] | |
| - | + | [[Category: Nikonov SV]] | |
| - | + | [[Category: Nikulin AD]] | |
| - | + | [[Category: Stolboushkina EA]] | |
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Current revision
The structures of aIF2gamma subunit from the archaeon Sulfolobus solfataricus in the GDP-bound form.
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