2d74

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of translation initiation factor aIF2betagamma heterodimer

Structural highlights

2d74 is a 2 chain structure with sequence from Pyrococcus furiosus DSM 3638. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.8Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

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

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^[1]

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

References

↑ Sokabe M, Yao M, Sakai N, Toya S, Tanaka I. Structure of archaeal translational initiation factor 2 betagamma-GDP reveals significant conformational change of the beta-subunit and switch 1 region. Proc Natl Acad Sci U S A. 2006 Aug 29;103(35):13016-21. Epub 2006 Aug 21. PMID:16924118

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/2d74"

@@ Line 3: / Line 3: @@
 <StructureSection load='2d74' size='340' side='right'caption='[[2d74]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2d74]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D74 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D74 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2d74]] 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=2D74 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D74 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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]] 2.8&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PF1717 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU]), PF0481 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=2d74 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d74 OCA], [https://pdbe.org/2d74 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d74 RCSB], [https://www.ebi.ac.uk/pdbsum/2d74 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d74 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). [[https://www.uniprot.org/uniprot/IF2B_PYRFU IF2B_PYRFU]] eIF-2 functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA (By similarity).
+[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]]
@@ Line 15: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d7/2d74_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 34: / Line 34: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Pyrfu]]
+[[Category: Pyrococcus furiosus DSM 3638]]
-[[Category: Sakai, N]]
+[[Category: Sakai N]]
-[[Category: Sokabe, M]]
+[[Category: Sokabe M]]
-[[Category: Tanaka, I]]
+[[Category: Tanaka I]]
-[[Category: Toya, S]]
+[[Category: Toya S]]
-[[Category: Yao, M]]
+[[Category: Yao M]]
-[[Category: Protein complex]]
-[[Category: Translation]]

2d74

From Proteopedia

Current revision

Crystal structure of translation initiation factor aIF2betagamma heterodimer

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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