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| | ==Crystal structure of the tRNA domain of tmRNA from Thermus thermophilus HB8== | | ==Crystal structure of the tRNA domain of tmRNA from Thermus thermophilus HB8== |
| - | <StructureSection load='2czj' size='340' side='right' caption='[[2czj]], [[Resolution|resolution]] 3.01Å' scene=''> | + | <StructureSection load='2czj' size='340' side='right'caption='[[2czj]], [[Resolution|resolution]] 3.01Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2czj]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CZJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CZJ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2czj]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CZJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CZJ FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</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]] 3.01Å</td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2czj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2czj OCA], [http://pdbe.org/2czj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2czj RCSB], [http://www.ebi.ac.uk/pdbsum/2czj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2czj ProSAT], [http://www.topsan.org/Proteins/RSGI/2czj TOPSAN]</span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</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=2czj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2czj OCA], [https://pdbe.org/2czj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2czj RCSB], [https://www.ebi.ac.uk/pdbsum/2czj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2czj ProSAT], [https://www.topsan.org/Proteins/RSGI/2czj 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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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Thet8]] | + | [[Category: Large Structures]] |
| - | [[Category: Bessho, Y]] | + | [[Category: Thermus thermophilus HB8]] |
| - | [[Category: Murayama, K]] | + | [[Category: Bessho Y]] |
| - | [[Category: Structural genomic]] | + | [[Category: Murayama K]] |
| - | [[Category: Sekine, S]] | + | [[Category: Sekine S]] |
| - | [[Category: Shibata, R]] | + | [[Category: Shibata R]] |
| - | [[Category: Shirouzu, M]] | + | [[Category: Shirouzu M]] |
| - | [[Category: Yokoyama, S]] | + | [[Category: Yokoyama S]] |
| - | [[Category: 10sa rna]]
| + | |
| - | [[Category: National project on protein structural and functional analyse]]
| + | |
| - | [[Category: Nppsfa]]
| + | |
| - | [[Category: Rna binding protein-rna complex]]
| + | |
| - | [[Category: Rsgi]]
| + | |
| - | [[Category: Smpb]]
| + | |
| - | [[Category: Ssra rna]]
| + | |
| - | [[Category: Tmrna]]
| + | |
| - | [[Category: Trans-translation]]
| + | |
| - | [[Category: Trna]]
| + | |
| Structural highlights
Function
SSRP_THET8 Binds specifically to the SsrA RNA (tmRNA) and is required for stable association of SsrA with ribosomes (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
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Bessho Y, Shibata R, Sekine S, Murayama K, Higashijima K, Hori-Takemoto C, Shirouzu M, Kuramitsu S, Yokoyama S. Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA. Proc Natl Acad Sci U S A. 2007 May 15;104(20):8293-8. Epub 2007 May 8. PMID:17488812
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