1wjx: Difference between revisions

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<StructureSection load='1wjx' size='340' side='right'caption='[[1wjx]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
<StructureSection load='1wjx' size='340' side='right'caption='[[1wjx]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1wjx]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WJX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1WJX FirstGlance]. <br>
<table><tr><td colspan='2'>[[1wjx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WJX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WJX FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</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]] 1.7&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TT0801 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1wjx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wjx OCA], [http://pdbe.org/1wjx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wjx RCSB], [http://www.ebi.ac.uk/pdbsum/1wjx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wjx ProSAT], [http://www.topsan.org/Proteins/RSGI/1wjx TOPSAN]</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=1wjx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wjx OCA], [https://pdbe.org/1wjx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wjx RCSB], [https://www.ebi.ac.uk/pdbsum/1wjx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wjx ProSAT], [https://www.topsan.org/Proteins/RSGI/1wjx TOPSAN]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/SSRP_THET8 SSRP_THET8]] Binds specifically to the SsrA RNA (tmRNA) and is required for stable association of SsrA with ribosomes (By similarity).  
[https://www.uniprot.org/uniprot/SSRP_THET8 SSRP_THET8] Binds specifically to the SsrA RNA (tmRNA) and is required for stable association of SsrA with ribosomes (By similarity).
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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=1wjx 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=1wjx ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
tmRNA and small protein B (SmpB) are essential trans-translation system components. In the present study, we determined the crystal structure of SmpB in complex with the entire tRNA domain of the tmRNA from Thermus thermophilus. Overall, the ribonucleoprotein complex (tRNP) mimics a long-variable-arm tRNA (class II tRNA) in the canonical L-shaped tertiary structure. The tmRNA terminus corresponds to the acceptor and T arms, or the upper part, of tRNA. On the other hand, the SmpB protein simulates the lower part, the anticodon and D stems, of tRNA. Intriguingly, several amino acid residues collaborate with tmRNA bases to reproduce the canonical tRNA core layers. The linker helix of tmRNA had been considered to correspond to the anticodon stem, but the complex structure unambiguously shows that it corresponds to the tRNA variable arm. The tmRNA linker helix, as well as the long variable arm of class II tRNA, may occupy the gap between the large and small ribosomal subunits. This suggested how the tRNA domain is connected to the mRNA domain entering the mRNA channel. A loop of SmpB in the tRNP is likely to participate in the interaction with alanyl-tRNA synthetase, which may be the mechanism for the promotion of tmRNA alanylation by the SmpB protein. Therefore, the tRNP may simulate a tRNA, both structurally and functionally, with respect to aminoacylation and ribosome entry.
Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA.,Bessho Y, Shibata R, Sekine S, Murayama K, Higashijima K, Hori-Takemoto C, Shirouzu M, Kuramitsu S, Yokoyama S Proc Natl Acad Sci U S A. 2007 May 15;104(20):8293-8. Epub 2007 May 8. PMID:17488812<ref>PMID:17488812</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1wjx" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Bessho, Y]]
[[Category: Thermus thermophilus]]
[[Category: Structural genomic]]
[[Category: Bessho Y]]
[[Category: Shibata, R]]
[[Category: Shibata R]]
[[Category: Shirouzu, M]]
[[Category: Shirouzu M]]
[[Category: Yokoyama, S]]
[[Category: Yokoyama S]]
[[Category: Rna binding protein]]
[[Category: Rsgi]]

Latest revision as of 13:31, 13 March 2024

Crystal sturucture of TT0801 from Thermus thermophilus

1wjx, resolution 1.70Å

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