2dcu: Difference between revisions
New page: left|200px<br /><applet load="2dcu" size="450" color="white" frame="true" align="right" spinBox="true" caption="2dcu, resolution 3.40Å" /> '''Crystal structure of... |
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== | ==Crystal structure of translation initiation factor aIF2betagamma heterodimer with GDP== | ||
<StructureSection load='2dcu' size='340' side='right'caption='[[2dcu]], [[Resolution|resolution]] 3.40Å' scene=''> | |||
[[ | == Structural highlights == | ||
[[ | <table><tr><td colspan='2'>[[2dcu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DCU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DCU 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]] 3.4Å</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2dcu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dcu OCA], [https://pdbe.org/2dcu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dcu RCSB], [https://www.ebi.ac.uk/pdbsum/2dcu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dcu ProSAT]</span></td></tr> | ||
[ | </table> | ||
[[ | == Function == | ||
[ | [https://www.uniprot.org/uniprot/IF2G_PYRFU IF2G_PYRFU] eIF-2 functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA (By similarity). | ||
[[ | == 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/dc/2dcu_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=2dcu ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Archaeal/eukaryotic initiation factor 2 (a/eIF2) consists of alpha-, beta-, and gamma-subunits and delivers initiator methionine tRNA (Met-tRNA(i)) to a small ribosomal subunit in a GTP-dependent manner. The structures of the aIF2betagamma (archaeal initiation factor 2 betagamma) heterodimeric complex in the apo and GDP forms were analyzed at 2.8- and 3.4-A resolution, respectively. The results showed that the N-terminal helix and the central helix-turn-helix domain of the beta-subunit bind to the G domain of the gamma-subunit but are distant from domains 2 and 3, to which the alpha-subunit and Met-tRNA(i) bind. This result is consistent with most of the previous analyses of eukaryotic factors, and thus indicates that the binding mode is essentially conserved among a/eIF2. Comparison with the uncomplexed structure showed significant differences between the two forms of the beta-subunit, particularly the C-terminal zinc-binding domain, which does not interact with the gamma-subunit and was suggested previously to be involved in GTP hydrolysis. Furthermore, the switch 1 region in the gamma-subunit, which is shown to be responsible for Met-tRNA(i) binding by mutational analysis, is moved away from the nucleotide through the interaction with highly conserved R87 in the beta-subunit. These results implicate that conformational change of the beta-subunit facilitates GTP hydrolysis by inducing the conformational change of the switch 1 region toward the off state. | |||
Structure of archaeal translational initiation factor 2 betagamma-GDP reveals significant conformational change of the beta-subunit and switch 1 region.,Sokabe M, Yao M, Sakai N, Toya S, Tanaka I Proc Natl Acad Sci U S A. 2006 Aug 29;103(35):13016-21. Epub 2006 Aug 21. PMID:16924118<ref>PMID:16924118</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2dcu" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Pyrococcus furiosus DSM 3638]] | |||
[[Category: Sakai N]] | |||
[[Category: Sokabe M]] | |||
[[Category: Tanaka I]] | |||
[[Category: Toya S]] | |||
[[Category: Yao M]] | |||
Latest revision as of 10:50, 23 October 2024
Crystal structure of translation initiation factor aIF2betagamma heterodimer with GDPCrystal structure of translation initiation factor aIF2betagamma heterodimer with GDP
Structural highlights
FunctionIF2G_PYRFU eIF-2 functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA (By similarity). 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 PubMedArchaeal/eukaryotic initiation factor 2 (a/eIF2) consists of alpha-, beta-, and gamma-subunits and delivers initiator methionine tRNA (Met-tRNA(i)) to a small ribosomal subunit in a GTP-dependent manner. The structures of the aIF2betagamma (archaeal initiation factor 2 betagamma) heterodimeric complex in the apo and GDP forms were analyzed at 2.8- and 3.4-A resolution, respectively. The results showed that the N-terminal helix and the central helix-turn-helix domain of the beta-subunit bind to the G domain of the gamma-subunit but are distant from domains 2 and 3, to which the alpha-subunit and Met-tRNA(i) bind. This result is consistent with most of the previous analyses of eukaryotic factors, and thus indicates that the binding mode is essentially conserved among a/eIF2. Comparison with the uncomplexed structure showed significant differences between the two forms of the beta-subunit, particularly the C-terminal zinc-binding domain, which does not interact with the gamma-subunit and was suggested previously to be involved in GTP hydrolysis. Furthermore, the switch 1 region in the gamma-subunit, which is shown to be responsible for Met-tRNA(i) binding by mutational analysis, is moved away from the nucleotide through the interaction with highly conserved R87 in the beta-subunit. These results implicate that conformational change of the beta-subunit facilitates GTP hydrolysis by inducing the conformational change of the switch 1 region toward the off state. Structure of archaeal translational initiation factor 2 betagamma-GDP reveals significant conformational change of the beta-subunit and switch 1 region.,Sokabe M, Yao M, Sakai N, Toya S, Tanaka I Proc Natl Acad Sci U S A. 2006 Aug 29;103(35):13016-21. Epub 2006 Aug 21. PMID:16924118[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References |
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